


The Difference Engine

by copperbadge



Category: Stargate Atlantis
Genre: Alternate Universe, Artificial Intelligence, Cyborgs, M/M, Programming, Robot Feels, Robots
Language: English
Status: Completed
Published: 2008-10-03
Updated: 2008-10-03
Packaged: 2017-11-19 03:15:02
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 5
Words: 22,031
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/568453
Author URL: https://archiveofourown.org/users/copperbadge/pseuds/copperbadge
Summary: <blockquote class="userstuff">
              <p>Sheppard remembered dying in Afghanistan, but since he was still walking around he didn't pay that memory too much mind.</p>
            </blockquote>





	1. Tria Prima

**Author's Note:**

> Thanks to Dove for Sheppard's euphemism translations, and to every SGA fan on my LJ for proclaiming there were tons of Sheppard Is A Robot fics, which turned out to be a cruel and unusual lie.

**Tria Prima:**  
 _An alchemical theory put forth by Paracelsus,_  
 _that the universe is composed of three elements:_  
 _Salt, Mercury, and Sulfur. In human terms,_  
 _salt represented the body..._

John Sheppard died in Afghanistan.

He remembered dying. He brushed it off as a psychological glitch, some kind of sympathetic reaction to Holland's death, a coping mechanism that let him get past survivor's guilt and failed rescuer's guilt and my friend's fucking dead okay guilt. He remembered taking fire, a bullet in his shoulder and one in his torso, piercing the liver, killing him, despite the fact that he hadn't been shot at all and had only taken a head injury, which left a scar but nothing more.

One of the base psychologists told him the liver was the seat of anger in some eastern religion or other, he hadn't been paying much attention. He was clearly angry at Holland for getting shot and himself for failing and the military for not backing him. Except really he wasn't, he was just sort of numb.

He was stuck on base through recuperation for the injury he did take and until the board reviewed his actions, but they let him keep flying, training hours with babyfaced kids and the occasional supply run, nothing in combat, nothing close to combat. The psychologists and doctors kept an eye on him, and he had a tendency to drift into the mechanic shop and fuck around with engines out of boredom, but in all it wasn't so bad. They cleared him for flight again, he flew again. Finished his tour. Got the _fucking hell_ out of that godforsaken desert.

He'd felt like he could never get cool again, like he was going to spend his life eating sand and hot wind. He didn't care about winning the war, didn't hate the Afghanis or the Iraqis or anyone, he'd just wanted to fly fast things. Getting out was okay by him.

He put in a request for remote duty and found himself transferred to McMurdo. Antarctica. Cold. _Awesome_.

General O'Neill's handshake felt oddly comfortable and his face was familiar; he had a moment where he was uncomfortable that he couldn't place the General, but then he brushed it off as irrelevant, not like O'Neill would remember him anyway. And nothing mattered really except getting in the air, getting the helicopter up and fighting the wind and the updrafts on his way out to the science station. They didn't talk a whole lot.

Until a giant glowing penis with tentacles tried to kill them.

"Hey, so, that thing back there," Sheppard said, sounding more anxious than he felt, which was not anxious at all really.

"Drone," O'Neill grunted, as the elevator began to descend.

"Am I the only one who thinks it looks like a giant glowing cock?" John asked.

O'Neill chuckled. "No. And don't tell anyone about it."

"I don't think anyone's going to believe I used evasive maneuvers on a flying giant cock, sir."

"That's the spirit," O'Neill said as they stepped into the science station. There was a brief look in his eyes, something clinical and studious, but it didn't last. He just got waylaid by some guy in glasses and told John not to touch anything and disappeared.

John looked around, scanned the faces and bodies, came to a conclusion: he was the new kid at school and it was lunchtime. Nobody was looking at him but everyone was watching him. Still, there was plenty to see down here, and he figured if he tried to do something that would blow them all up someone would stop him, so he wandered. Which was how he overheard a man talking about firing and deactivating the -- drone -- and discovered who his would-be attacker was. He really did want to be angry at Carson Beckett for being the reason he and General O'Neill were late that morning, but Beckett apologised and anyway he seemed like a nice guy, so after an initial flare of...of something, John let it go and took to studying the cool art-deco chair next to him. It was pretty interesting.

The impulse didn't come from anywhere conscious, but seriously, how dangerous could it be to sit in a chair?

A chair that moved and sucked his head back and propped his feet up and ooooh. Power.

He felt it not so much in a tingle along his skin or a sharpness in his spine but in binary dancing in front of his eyes and the feeling...as though he'd been on battery power and someone had just plugged him into the wall. When the sensation finally leveled off he found there were new faces in front of him, new but familiar -- a dark-haired woman and a pale man who talked faster than anyone John had ever met.

He knew that name almost as soon as it was spoken -- Doctor Rodney McKay. There was an intense familiarity about McKay, stronger even than O'Neill, but it wasn't like John got thrown together with astrophysicists very often and McKay would be kind of hard to forget.

He reached out to shake Dr. Weir's hand.

"Pleasure to meet you, John Sheppard," she said with a smile. An uncontrollable urge to _protect_ her washed over him, startling him -- he hadn't felt anything that intense in months. And goddammit, really, where had he met McKay before? McKay acted like he knew him, knew his rank before General O'Neill even introduced him.

_Major, think about where we are in the solar system._

***

The meeting never happened. Definitely not.

McKay didn't sit in the chair and stir sugar into his coffee while O'Neill wasn't reading through a results brief and studying the accompanying informative printouts.

"All right, McKay," O'Neill said. "You've convinced me. Weir wants him to come on the mission."

McKay grinned. "Yeah, I know."

"How'd you know he'd have the gene?"

"Ah, well, we got lucky," McKay said. "It was flagged in his file. Strongest we've found yet -- "

"Enough crowing. You get to take your toy with you, just try not to break him."

"Short of death he's pretty difficult to break," McKay replied smugly. "The microwires might show up in an autopsy but not before, and if he takes a direct head-hit we'll have worse things to worry about than the cybernetics, but other than that..."

"You know, I've seen this movie, I don't think it ends well," O'Neill continued. "You didn't build lasers into his eyes or anything?"

McKay rolled his eyes. "He's autonomous, like any human being. We've programmed some...suggestions into his subroutines, and I'm not sure the emotions AI is functioning properly, but he'll chalk that up to PTSD if he thinks about it."

"You are one fucked-up mad scientist, you know that?"

"You asked me to build you a robot, General. I built you a robot. It's not my fault he's more useful to me than to you."

***

_To the day she died Elizabeth Weir didn't know that John Sheppard had died in Afghanistan. There was no reason for her to know. McKay would have felt guilty about this, but he suspected if she knew she'd eventually find out about the subroutine he wrote into Sheppard, the one that urged him to protect Elizabeth at all costs, and that knowledge just couldn't take any of them anywhere good._

_The Executive Safety routine was superceded only by the Common Defence one he'd written in after arrival: Protect Atlantis._

_It was very complex code._

***

The longer John spent with the people of Atlantis, the tighter he would bond with them as his neural net engaged its facial-recognition patterns and began filing away data to be incorporated into his Charisma circuitry. The preliminary test had been beyond Rodney's wildest expectations -- he'd integrated seamlessly into McMurdo, accepted the research station without hesitation, and lit up the Control chair like a Christmas tree. Aside from requiring some _coaxing_ from O'Neill to join the mission (the Obedience program couldn't be too firm or he'd just be an idiot soldier, but it responded most strongly to General O'Neill), John was well ahead of the curve.

In the first few days after the raising of Atlantis there was a sort of informal Senior Staff dinner each night; not so much that they all wanted to sit together, as that they all knew that it made the underlings uncomfortable if the bosses sat with them. McKay sat on one side of Elizabeth, Bates on the other, Carson and the head of Botany, McKay couldn't be fucked to remember her name, across from them.

"You know I think this is the first time I've seen Major Sheppard eat in the mess?" Elizabeth remarked, gently indicating with her fork as Sheppard sniffed an apple, tucked it under his arm with a water bottle, and inspected the sandwiches.

"He's had a lot of catching up to do," Bates said stiffly.

"We should ask him over," Elizabeth suggested. Carson glanced at McKay and they shared a grin.

"I don't know," Botany Woman said. "Does he seem kind of...chilly to you?"

"No, not at all," Elizabeth looked surprised. Under the table, Carson kicked McKay in the shin triumphantly. "He's been nothing but friendly with me. I think we'll work well together."

"He's not bad," Bates put in.

"Hey! Sheppard!" McKay called, waving his spoon in the air. Sheppard's head whipped up sharply. It was true that there was a certain...intensity of gaze that could probably be tweaked, but McKay wasn't comfortable working on pure aesthetics just yet. There had been that one time with the early prototypes when someone decided a seduction subroutine would be a good idea and Zelenka had blown out three monitors trying to contain it.

"McKay," Sheppard said in measured tones.

"Come, eat. Do you want all that sandwich?"

This time Carson's kick was scolding.

"Nah," Sheppard said, offering him half.

"Thanks," McKay said, ignoring Carson's glare.

***

"And we have...sleep," McKay called, tapping on the laptop's keys. He'd remarked to Carson once, in a moment of downtime between surgeries, that he'd played piano as a child. Carson could believe it; McKay typed a hundred and forty words per minute (a hundred and thirty if the keyboard was unfamiliar), and you didn't get that kind of dexterity by accident. "Initiating remote connection."

"Body looks good," Carson remarked, studying a monitor nearby where Sheppard's brain was feeding vitals over the wireless from his bedroom to the lab. "Cell repair's holding, respiration slowing, heart rate is pretty constant."

"Jeez, will you look at that," McKay said, pointing to his screen. "His neural efficiency is increasing."

"He's compiling," Zelenka suggested.

"Well, that's basically what we do, isn't it," Carson answered. "Compiling, I mean. Dreams. Working through the day, resetting the brain."

"Mmm, your analogies are pretty and so completely wrong," McKay said, entirely without rancor. "How are the neural interfaces holding up?"

"Just fine, Rodney," Carson sighed. "There's no tissue incursion."

"I think we maybe call this an unqualified success," Zelenka said, giving McKay a satisfied look.

"No success is ever unqualified."

"You? Are a pessimist."

"Of course I am." McKay was still studying his screen. "That way, when nice things happen, I'm pleasantly surprised."

Carson moved to stand behind the two men, comprehending perhaps a quarter of the readouts on their screens. He could barely code HTML, let alone rewire a cybernetic brain; his job was to keep John Sheppard's body alive and make sure the muscles and mechanics didn't interfere with one another in any way they weren't supposed to.

He knew every inch of John's body; he'd laid every microwire, patched up all three bullet wounds, led every major surgery on the Major's mortal shell. And from where he stood, his work was done. Any medical attention paid to John Sheppard henceforth would be strictly for injuries he had yet to receive.

"Boys," he said, clapping each of them on the shoulder, "It's been a long day. I am going to officially hand off the care and feeding of Major John Sheppard. Consider the medical withdrawn, with compliments."

"Is not much more to be done here," Zelenka agreed.

"Weekly monitoring," McKay replied. "We can cut it down to weekly. Oh," he added, intrigued.

"What?" Zelenka asked.

"Here," McKay isolated a spiky graph and tapped it. "The ATA gene's opening up his nets. He's crossing data storage and recall."

"What's that mean?" Carson inquired.

"He's learning," McKay said proudly. "He's learning how to use his gene. This is great, until now he's just been storing memory. Now he's trying to cross-reference it and spontaneously generate new knowledge."

"Not trying, doing," Zelenka added.

"Congratulations," Carson said. "It's a boy."

***

_It started as Radek's hobby, Artificial Intelligence, and blossomed when he was admitted to the Stargate program. The Ancients had a handle on AI technology, but didn't seem to make much use of it; between their hardware and the new software coming out of the top programming schools, Radek really just wanted to see if he could get a top-notch Sims game going. When McKay got bored (frequent!) he would join in, helping write new code, helping write code that would allow the program to write its own code._

_Radek called it a virus and infected a small wheeled robot with it, the kind they were building at MIT. The robot had four wheels, four arms, an infrared sensor, and about a gig of memory. They left it alone for the night, left it on to see what it would do, and in the morning it had two more arms and a display screen for ease of communication, and they were down a monitor and half their spare parts._

_"Hoo, boy," Radek said, looking at McKay. "Now we write a grant proposal, yes?"_

***

"Don't you ever get scared?" Ford asked him once, on one of their early missions. Teyla and McKay were both asleep on the other side of the fire, and technically it was Ford's watch, but John wasn't particularly tired and he knew how boring watch was.

"Sure," John lied. "All the time. Especially in Afghanistan." He could remember being scared in Afghanistan, at least.

"Because you sure act like you know you're invincible."

"Well, it freaks people out," John said.

"Yeah, it freaks me out."

"Nobody said you had to be a smartass like me," John replied. "Do your own thing, Ford. Whatever gets you through the tour."

Ford grinned. "Now you sound like my grandad."

"Is he Semper Fi?"

"He was, yeah." Ford shrugged. "I'd just like to be able to look at someone pointing a gun at me and think, _yeah, bring it._ "

"Well, the worst that can happen is you die," John said easily.

Ford looked at him, frowning, and John wondered what he'd said.

"That's not bad enough?" Ford asked.

"Nah," John answered, thinking of the memory of dying in Afghanistan.

"You believe in Heaven?"

"Don't care." John poked the fire with a stick, pinpointing the precise faultline on one of the logs, causing a huge gout of fresh flame to burst upwards.

"And you think death's not so bad, huh?" Ford challenged.

"I don't really think about it at all," John said. "Huh."

"Huh?"

"That's weird, isn't it?" he asked, a note of uncertainty in his voice.

"Whatever gets you through the tour, sir."

In the complex corners of John's brain, there is a line of code. Most of his programming isn't if-then, because they'd need millions of those for every possible situation. It is a complex network of mathematical probabilities and calculation formulas. Still, this one line, because it is important, is pretty basic.

_When all other options have been exhausted and it is in the best interests of the general population to do so, suicide to ensure the safety of the population is mandated._

McKay never realised this would erase the fear of death, nor that John's innate adaptable programming would extend this mercy to others, as well. McKay called it the killswitch, but it would have been more apt to call it the Mercy-Killing Code.

***

There was a No Mercy Code as well. That one John wrote himself, subconsciously, because while the Executive Safety code provided him with the impetus to protect Elizabeth (or any future leader of the Atlantis mission) it didn't leave him a lot of instructions on how to do so.

He was fully aware that you shouldn't feel _nothing_ after killing a platoon of enemy soldiers by flicking a switch, but nobody else seemed particularly bothered by it.

Still, his recognition software had identified Dr. Heightmeyer as a potential diagnostic tool, and the sensation of discomfort over not feeling greater discomfort obviously indicated something was wrong with him.

"Was there something you wanted to talk about specifically?" she asked, as John fidgeted with his hands and pulled reluctant faces. Deep inside him something was telling him that a direct interface would be so much easier than language synthesis, which was imprecise.

"Yeah," he said. "I killed a lot of people during the storm, when the Genii tried to take Atlantis."

She nodded. He considered what other details to share.

"They were the enemy," he added.

"Does that make you conflicted at all?" she asked.

"Not really," he answered reluctantly. "It's more the whole...lack of conflict."

She tilted her head. "You feel good about killing people?"

"I just don't feel very bad about it."

"Because they were the enemy?"

"You still feel bad about killing people when they're the enemy," he answered, remembering the sick sensation the first time he'd realised that a weapon he'd just fired had actually taken another person's life. He didn't feel very sick anymore. "Or you should, anyway."

"Why do you think you should?"

"Because people do." This was completely and totally useless.

"How do you know?"

"I just know," he replied. "It's implicit. You kill people, you feel bad about it. That's some kind of instinct, right?"

"And you feel bad because you don't feel bad about killing people?" she asked.

"Well, it's not healthy," he said, already calculating how long this session was supposed to be. Potential diagnostic tool, his ass.

"But you're seeking help for it," she said. "That's good, don't you think?"

"It's what you're supposed to do."

"You believe strongly in what you're supposed to do."

"Yeah, that's..." dim frustration loomed. "Yeah."

She nodded. "How can I help?"

He sat for a while. Seriously? Here he was, saying he couldn't fix this on his own, and she was telling him she wanted him to tell her how to fix it.

"Also I don't think I have dreams anymore," he announced. She raised an eyebrow, but he knew she would let it slide.

"Everyone has dreams, John," she said. "We don't always remember them -- "

"I haven't had a dream I can remember since I left Afghanistan. Maybe before." Definitely before, but he didn't think the lack of dreams was attributable to Holland dying, especially since that kind of thing was supposed to give you nightmares.

"Well, we can work on that," she said. "We'll start small, with that, okay?"

"Okay." And she gave him ten thousand stupid little mental tricks to help him find out when he was dreaming, like counting his fingers and looking at clocks and setting his alarm so that he'd wake up out of REM sleep.

Then he got up and said thank you and went to see McKay and McKay waved his hands at him and said _who fucking cares? Do you really miss dreaming? Do you really want to be miserable because you killed a bunch of guys who incidentally were being led by a sociopathic megalomaniac who knifed me?_ which was infinitely more reassuring because actually, all those things were facts. He didn't want to be unhappy that he'd kicked the shit out of the bad guys and he didn't really care about dreams for the sake of dreams, and if McKay could think weird shit like that it must be all right. Not that McKay was a baseline for sanity or anything, but he was a pretty pragmatic guy.

Dropped down from weekly to monthly checks, McKay found some of this logic in John's base code and felt inordinately proud.

***

_Prime-Not!Prime was invented to test the neural net's calculating speed, played first on a computer interacting directly with a neural construct not yet installed in John Sheppard's brain-dead body (which at the moment housed a perfectly alive brain and was tooling around Afghanistan blowing shit up). As the calculating speed reached human reaction-time and then surpassed average human reaction time, Zelenka looked more and more pleased. They introduced a randomiser, so that every once in a while it would get one wrong, because humans weren't infallible. Rodney programmed the randomiser into his social interactions as well, paired with the Charisma circuit. Eventually this meant that occasionally Sheppard said something deeply awkward. It also seemed to affect his ability to read and react to body language, but only in intense situations._

_In those early days in Atlantis they egged Sheppard into the game because they wanted to make sure nothing was degrading as line after line of new programming appeared in the monthly checkups. It caught on among the scientists as an actual game. Rodney enjoyed it._

***

Carson tried not to show how familiar he was with John's body, every time the Major came to him for a patch-up from sparring or some hell he'd caught out in the field. It was doubtful John would have noticed, but there was no need to call attention to the almost microscopically thin scars where arm met shoulder, where leg met hip, where spine met sternum, even as his hands instinctively found them and made sure they were still stable.

"How does it feel?" he asked, knowing full well that the fibula was fractured.

"Not too bad. Stiff," Sheppard replied, flexing a muscle. The microwires would have tightened around the bone, immobilising it and setting it at the same time. No need for a cast, and the wires would take the weight off the bone itself.

"Pain? Out of ten?"

"Three," which was Military for Five, and there were jokes to be made about soldiers' ability to count, but Carson let them slide. Perhaps the wires were clenching off the nerves, too.

"I think it's a slight sprain. Keep it elevated for a few days. No running, and try to stay off it. I'll give you a brace," he added.

"Sexy," Sheppard sighed.

"They are, actually. Women love a helpless man," Carson said. When he looked up from his tablet, Sheppard had a thoughtful, perplexed expression on his face. "Surely you don't need any assistance in that regard, however?" he asked delicately.

"It explains a few things," Sheppard replied.

"Such as?"

"Do you think oblivious counts as helpless?"

Carson grinned at him, parentally proud. "Having fun in the Pegasus Galaxy, are we?" he asked, and turned to fetch a few condoms out of the supplies locker along with the brace-bandage. Sheppard caught one of them between his fingers, held it up, frowned.

"If you make me demonstrate on a cucumber I'm going to be very put out," Carson observed. Sheppard tucked the foil packet against his palm and shook his head with a slight smile.

"Just remember to get her name and try not to seed the galaxy with obscenely talented black-haired daredevils," Carson told him, and clapped him on the back and sent him on his way.

McKay once asked Carson if he thought Sheppard would be, you know, _capable_ , and he'd replied easily, "Why not? It's an autonomic response to pleasure. We've got the fully organic brains we were born with and we can hardly control the damn things, so I don't see why he shouldn't be able to. He can feel pleasure, can't he? In the brain?"

"Oh, there are algorithms," Zelenka had said dismissively. "Linked in to the socialisation and achievement modules. He should feel pleasure when he does something correctly. Intellectual pleasure," he amended, when Carson gave him a horrified look.

***

Rodney saw definite signs of pleasure in Sheppard's reaction when he was promoted to Lieutenant Colonel, just barely within the acceptable service-years range. He knew from years at the SGC that not many people, and nobody with a mark on their record, made LtC promotion the first year they were eligible for it. But, there was Lieutenant Colonel John Sheppard. And he was _beaming_.

"I don't even know why, you know?" Sheppard said, practically vibrating with pride as he sat at the cafe table in his full dress regalia. "Why it's so satisfying. It's not like I ever cared about this stuff."

"Well, you," Rodney said, and then didn't have anything else to say, so he stopped talking.

"I mean I wasn't competing with anyone. Besides, it's not like it means anything when you're already military commander of a city. Garrison? We're a garrison, aren't we? Maybe an outpost."

Rodney grinned a little into his coffee cup. "You're not itching to dig up a phone book and call all your old Air Force pals and gloat?"

"Nah. And nobody here knows what it means. Civilians never do. Except that I'm in uniform."

There was a Purple Heart ribbon on his pin insignia, a plain purple strip. Out here near the mountain, they got a lot of ex-military around; the man pouring the coffee noticed the ribbon too, and Rodney doubted Lieutenant Colonel Sheppard was paying for his meal today.

"It just feels good," Sheppard said. There was a slight undertone in his voice that Rodney didn't immediately grasp; Sheppard was watching him, glancing at the saltshaker, at the other diners, back to him.

"Oh, for fuck's sake," he said, when the penny dropped. Sheppard wanted to be _petted_. "Yes, Lieutenant Colonel, we're all very proud of you, I think you're just the bee's knees. Men want to be you, women want to be with you. Happy now?"

"You have to call me Colonel. You have to introduce me to everyone we meet: _This is my friend, Colonel John Sheppard_ ," he said, holding out a hand to an imaginary person sitting next to him and gesturing with his other to indicated said imaginary person.

"Lieutenant Colonel," Rodney corrected, right before this is my friend hit him upside the head.

"Colonel," Sheppard insisted. "Proper military parlance, LtCs are addressed as Colonel in speech and correspondence."

"I'm not military, Lieutenant Colonel," Rodney retorted.

"Colonel."

"Lieutenant Colonel."

Sheppard growled, and Rodney rolled his eyes as dinner arrived.

 _This is my friend_. He warmed to the sentiment for a good three hours until it occurred to him that along with being a pretty nice thing to say it was also an indication that the Colonel's neural net had been reworking his base code again. Zelenka would be over the moon -- not only had their cyberboy with the clockwork brain survived a year in Atlantis, he was thriving and getting _promoted_.

It took almost the entire trip back on the Daedalus for Rodney to realise that he was going whole weeks at a time without thinking of the Major -- the Colonel -- as a machine or an experiment. This was, in fact, his friend, Colonel John Sheppard.

He wasn't quite sure how he felt about that.

He wondered what Sheppard had been like before the shooting.

***

_Zelenka and McKay argued for days via secured-server email about how the bug genes got into the neural net; Zelenka thought the mutations must have caused brain regrowth, putting pressure on the cybernetics, while McKay insisited that idea was stupid, something he'd picked up from a horror film, and that clearly it was just the altered bloodstream causing misfires where Sheppard's nerves interfaced with the electronics. Carson refused to settle the debate, citing doctor-patient priviledge for the first time since they'd activated Sheppard after the shooting._

_"He's hardly an experiment anymore," he said, and McKay and Zelenka both felt a little ashamed._

***

John liked Atlantis, much more than he'd liked pretty much anywhere else he'd lived. He liked knowing every face he saw in the corridors, and it was weird how much more people seemed to like him here. Maybe it was the allure of command.

He didn't like the stroganoff the mess served. He didn't like it when anything tried to attack his city or Elizabeth. He didn't like it when he and Elizabeth didn't agree. He didn't like the Wraith. He did like killing Wraith, and big explosions, and flying the puddlejumpers, and sitting with McKay and Zelenka at lunch. He didn't like it when someone hurt anyone on his team. He'd been over the moon when he got promoted, high with pride and achievement, but that lasted only a few hours before fading into faint, amused pleasure.

It all felt very muted, slightly unreal, none of it passionate, and he wondered if he was messed up, mentally. He liked this, he disliked that, but he didn't love or hate anything. Even the Wraith. He said he did, because that was requisite, everyone hated the Wraith, but he didn't really feel any burning emotions at all.

It was kind of nice, actually, not to feel fear anymore, or guilt over events he couldn't control. He felt uncomfortable when he did something he knew he shouldn't -- stole Rodney's pudding, or cheated a little when he was sparring with Ronon -- so at least he knew he still had a conscience. But even then it was like a twitch, not even a twinge.

In his second year on Atlantis and for the first time since Afghanistan, John felt something deep and searing and insatiable, and it was _anger_. Homicidal, paranoid anger, at least that was how he classified it later. After they'd detoxed him, after they'd pumped the bad bug genes out of his system and made him _human_ again, he remembered the flavour of anger on his tongue and the white-hot pressure in his head. It was ten kinds of unpleasant, it was very very uncomfortable, and it made something squirm deep inside him to know that he had almost turned on Elizabeth. Elizabeth, of all people.

It lingered for days, until finally she put down the report she was reading as he hovered near her table and told him in no uncertain terms to stop pestering her and get the hell over himself.

He decided he could cope with this numbness, whatever it was, if it meant never never never feeling anger like that again.

***

_John Sheppard did not remember being brain dead. Who would?_

_He remembered the day he filled out the paperwork for the military in the event of his death. He decided to donate his body to science, grinning a little because he was thinking of the old joke about donating his body to science fiction. He did not remember, because he'd been brain dead at the time, that McKay stood on one side of him and Carson stood on the other on the long plane flight from Afghanistan to Cheyenne Mountain where Zelenka was waiting with the Ancient technology and a cybernetic brain. Beckett was having a hand-wringing moment about the ethics of removing a man's bullet-scrambled brains and replacing them with a computer, and McKay said to him, "Suck it up. He's technically dead. He donated his body to science. We are science. We get the body."_

_John remembered dying from a bullet wound in the shoulder and one in the gut, but for him that never happened any more than the bullet that entered through his skull just behind his right ear and switched off his brain. The scars were gone and in the end he only lost about a week, which for all anyone in Afghanistan knew he spent recuperating from a head wound in the infirmary._


	2. Chapter 2

_...mercury represented the moral and creative spirit..._

Their first experiments with the Wraith retrovirus were uncomfortably reminiscent of the deception they'd practiced on Sheppard for almost two and a half years, and eventually Carson broke down and threw a fit.

"We have to tell him," he said, tossing his dinner tray down and leaning over it to speak to Rodney in hushed tones. "I'm not going to have another Michael on my hands."

"It's always about _him_ ," Rodney said to Zelenka, who sighed and pushed his glasses up.

"I'm serious, Rodney. He's acting independently, he's doing well, he survived six months without you delving into his base code -- "

"Eight months," Zelenka said. "We have not once meddled since he came back from his time-journey thing."

"All the more reason to tell him. He deserves to know he's wandering around with a calculator for a brain."

"That is grossly simplifying -- "

"Rodney!"

"Keep it down, will you?" Rodney hissed, glancing sidelong. Sheppard was sitting with Ronon and Elizabeth at one of the small tables, picking at the last of his meal and grinning.

"He's not a machine, he's a person, I know that," Carson said, lowering his voice. "And that's why he should know."

"You think he's not going to pull a Michael anyway when he finds out?" Rodney demanded.

"Listen, I did this because I thought it would help brain-damaged soldiers in the field. Nothing's been done about that since we left Earth. It's time to let the IOA decide if it's appropriate to start testing the technique on others. And we can't do that if we can't gauge the intellectual and emotional impact of discovery on the subject."

Zelenka frowned. "We cannot go off willy-nilly and announce, Colonel Sheppard, you are a clockwork man."

"Again with the simplifying," Rodney said, annoyed.

"You don't want to tell him because you think he'll be mad at you," Carson accused.

"Well, _yeah!_ " Rodney said. "Among other things, like the military commander of the entire operation freaking out and doing god-knows-what when he discovers he died in battle two years ago."

"We must tell O'Neill," Zelenka said. "Is not our decision to be made. We will take our case notes and send them to General O'Neill. _The Modern Prometheus_ , by Doctors Radek Zelenka and Rodney McKay and Carson Beckett."

"How come you get top billing?"

"Reverse alphabetical," Zelenka said beatifically.

"I think you two are being very callous about this," Carson announced.

"We just told you the plan," Rodney said. "We'll send the notes to O'Neill, ask him what he thinks, tell him you're hysterical, and do what he says. In the meantime, keep your mouth shut."

"I'm warning you, Rodney -- "

"Warn away," Rodney retorted. "Just stay away from Sheppard until we hear from O'Neill."

***

Jack leaned around the doorway of Daniel's office, waited until Daniel was finished with whatever he was working on, and held up a flashdrive to get his attention.

"Weekly databurst from Pegasus," he said, twirling the little drive between his fingers.

"Oh? Oh! Excellent," Daniel answered. "I've got snacks."

They commandeered one of the empty SGC conference rooms, because it had a projector and a screen. The mission reports themselves were usually text and Jack generally skimmed the summaries unless Elizabeth had flagged something for his attention, but in the past few months Colonel Sheppard had started sending regular video-briefings, which were often the highlight of the burst.

Sure enough, the first of three video-messages marked for the attention of General O'Neill was from Sheppard. He appeared on the screen, looking pretty healthy from what they could see of him, that Johnny Cash poster in the background as always.

"General O'Neill," he said, managing to seem solemn and amused at the same time. "And probably Dr. Jackson, good afternoon. This is your weekly informal briefing from the Pegasus Galaxy."

Sheppard's face was still youthful and also quite mobile; expressions came and went, though the General knew enough to look for whether or not they ever reached his eyes.

"I thought I'd dig up a few of the more interesting euphemisms from the reports for you, just in the interest of keeping everyone in the Milky Way on the same page," he said, looking down to study some notes offscreen.

"I love this part," Daniel said, popping a peanut into his mouth. Jack stole a handful from the bowl and leaned back.

"Okay, let's see. Uh. This is a good one," he said. " _Due to cultural differences, we were unable to reach mutually satisfactory diplomatic arrangements_. They wanted to marry me to the Prime Minister's daughter so we could have lots of ATA babies. See also, last time, _Colonel Sheppard has lodged a complaint regarding requests for duties outside the scope of his office_."

Daniel chuckled. "It's all about sex, in Pegasus."

"That's more about marriage, really," Jack pointed out. "Which is never about sex."

"If you say so."

Onscreen, Sheppard's lips quirked. "I took this one from one of the junior teams: _There were many opportunities for skills improvement_. I think that means _we really fucked this one up_ , but none of them will go into details. I expect to see a lot more of this phrase as word gets out about its usefulness. Also, one of the biology Ad Hocs noted that _Local fauna makes further exploration inadvisable_ which, turns out, involves a hilarious story about almost being eaten by Ents."

"Ents?" Jack asked Daniel.

"Lord of the Rings, talking trees. I'll fill you in later," Daniel said, not looking away from the screen.

"Last up in the hit parade, and my personal favourite of the week, Dr. McKay writes: _standard diplomatic techniques were at odds with local custom, requiring team improvisation_. Which is his way of saying he had to give his shirt to Teyla so nobody would stone her to death."

Jack snorted.

"She does like a breeze," Sheppard commented, and leaned back slightly. "Otherwise, there's not much to report that you won't be getting from Elizabeth. Morale's pretty good. McKay's been terrorising the department heads again, I'm not sure why. The Athosians seem happy, at least that's what Teyla says. We're getting some nice nights out here, though it's turning a little cold; I guess we're in for winter, soon. And the Marines would like me to say thank-you for the crate of Easy Mac that Dr. Jackson shipped on the last Daedalus run. For these guys it's like a taste of home."

"I...just thought..." Daniel caught Jack narrowing his eyes at him. "You know. Comfort food. And it's hard to get macaroni in the Pegasus Galaxy."

"You're buttering them up," Jack accused. "In case you ever go there, which you're not."

"He said morale is good! Do you want cranky Marines?"

"I don't want Marines at all."

Onscreen, Sheppard continued. "I'm preparing a list of digital files the boys and girls back here would like to get; you should get that next week, and I'm going to ask as a personal favour that you look the other way and indulge us as regards the repeated requests I've had for Earth pornography, since morale would definitely stay high if we could get that request filled. Pegasus would send some in trade but I'm afraid I accidentally erased that video recording we took on the Planet of the Penes. Um, you'll see that in the mission reports, I've included the entire intranet email debate about the proper pluralisation of Penis."

"Awesome," Daniel said. "John Sheppard speaks to an anthropologist's heart."

"That's all from Pegasus, I think; see you next week. Sheppard out."

Sheppard's arm came up for a brief second as he reached out to turn off the camera, and then there was darkness. Jack tapped a few commands into the laptop, pulling up the next file.

"Isn't that -- what's his name, the Czech?" Daniel said.

"Radek Zelenka. McKay's right-hand man."

"He looks a little crazed," Daniel agreed.

Zelenka looked like he had, at least, combed his hair and ironed a shirt for the occasion; Jack pressed the play button, curious.

"This is message for General Jack O'Neill, eyes-only," Zelenka said, apparently reading from a prompter on the screen. "It is concerning Project Tria Prima."

Jack casually flicked the stop button. Daniel glanced at him.

"What's Project Tria Prima?" he asked.

"Old study I used to supervise," Jack replied. "It's nothing important. But I think I'd better watch the rest of this in private."

Daniel gave him a curious look; they held the same security clearance, after all.

"It involves some medical confidentiality," he said. "Sorry, Daniel."

"No, that's fine -- I'll just -- " Daniel jerked a thumb over his shoulder at the doorway, as he stood. "I'm sure I've got stuff from Pegasus too."

Jack nodded, gave him a thin smile, and then locked the conference room door before returning to the laptop. He took the image off the projection screen, plugged in a set of headphones, and hit the play button again.

"Attached to this databurst you will find an encrypted copy of our notes regarding Tria Prima since its inception," Zelenka continued. "Dr. Beckett has had what Dr. McKay calls an attack of conscience. He wishes to inform the subject of the procedures performed on him and study his reaction."

Jack tilted his head. Zelenka looked unhappy, but that could just be because it was hard to look at John Sheppard and think, _the subject_.

"Dr. McKay and Dr. Beckett have written many pages on this topic," Zelenka said. "I am aware you are a busy man. I thought, I will present a summary for you, very brief, as Dr. McKay and Dr. Beckett wish a verdict from you on the appropriate action."

God bless Radek Zelenka.

He leaned back and listened and studied the charts Zelenka presented on screen, taking it in and thinking at the same time of Sheppard's lazy grin as he presented his unofficial brief. Sheppard liked to keep his boss on the same page as him and trusted Jack enough to share the casual stuff, like how the Marines were doing and what the weather was like. Jack had long since stopped looking for anything he associated with the word "robot", like jerky movements or a tinny uninflected voice or a megalomanic urge to take over the galaxy.

Zelenka completed his summary and chewed on his lip for a minute.

"As for my personal recommendation, I do not entirely know where to begin. Colonel Sheppard is a good man. In case we all die horribly, yes, he should know. He is not a man who attaches easily, however, and to find that his friends have lied to him..."

It went unsaid: to find out that his friends _built him_.

"...I do not know what he would do."

***

_Jack O'Neill knew a little bit about how to lie to yourself._

_The program had been put under his supervision because he asked for it and because he was a military man with a knowledge of alien tech. The original experiment had been given the grant to try and help brain-damaged combat veterans recover their faculties. The grant only allowed for one test subject, and it was understood that the minimum study length before second-phase testing would be five years. Dr. Beckett's assertion that after only two years he wanted to help other soldiers was therefore patently bullshit. Beckett felt bad they were lying to the robot._

_Jack knew at least a little about Sheppard's life; they were both Air Force and both SGC. He tried to decide how he would react in Sheppard's place, until he started wondering neurotically if maybe they'd slipped him a digital brain on the sly as well, at which point he gave up for the sake of his sanity._

_He waited six days, until he was under pressure to pass along anything he had for the next day's databurst, and then he sat in his office and set up a camera._

***

Radek was in favour of getting drunk. Or getting Sheppard drunk, but that was an expensive proposition because the amount of alcohol required to interrupt the easy flow of information where body met brain was severe.

McKay suggested locking him up before telling him, because he'd seen Sheppard in action. Beckett said absolutely not, and McKay derided him for his sudden compassion, as if a psych rotation in his youth qualified him to determine whether Sheppard would take being locked up in the wrong spirit. McKay had been wrist-deep in Sheppard's base code for a year and a half; he was best to judge.

"We're not locking him up, Rodney," Carson said.

"Well, we need to get him unarmed, at least," McKay replied. Radek rubbed the bridge of his nose.

General O'Neill had spoken to them in a distinctly non-military fashion about the philosophy of consciousness, the measure of sentience, and the rights of man, citing works that none of them would have thought the General would be familiar with and a couple that left even Radek scratching his head. O'Neill had pointed out that nobody really thought it would get this far, had they, and while the point was to see if Sheppard could reintegrate without self-consciousness that he was different, well, he _was_ different and also he questioned what any of them, including himself, had been thinking when they sent him to Pegasus.

"ATA," McKay replied to the recording. "And the fact that all three of us were going."

"He can't hear you," Radek pointed out.

" _I know that!_ "

In the end, they cleared one of Carson's exam rooms of anything pointy or dangerous and after dinner Beckett called him down to the infirmary. Sheppard showed up with a _what did I do now_ look on his face, took in the three of them sitting in the exam room, and grinned as he leaned in the doorway.

"Is this an intervention?" he asked. "Because I swear I've been clean for years, guys."

"Not precisely," Beckett said. "I think you'd better come inside."

Sheppard raised his eyebrows, but he stepped inside and pulled a chair around backwards, straddling it and resting his arms on the backrest.

"We need to tell you about a military experiment called Project Tria Prima," Beckett said. Radek swallowed. "It was intended to test the possibility of replacing all or part of a damaged brain with a cybernetic implant, using a combination of alien and Ancient technology."

"You can't test it on my Marines," Sheppard said.

"We don't want to test it on your Marines," Beckett answered patiently. "We -- "

"This is ludicrous and painful," McKay announced. He pointed at Sheppard. "Colonel, you're a robot."

Radek put his hand over his eyes. Beckett sighed.

"Well, I know I'm not the most touchy-feely guy in the world," Sheppard drawled.

"No, you're a robot. An actual robot. Your brain has blinking lights in it," McKay said.

Sheppard just watched them, warily.

"Much as it seems at the moment," Radek said, "we have not all mutually gone insane."

He pushed a tablet at Sheppard, who took it and studied the images there -- a handful of scans of the cybernetic brain, a detailed technical drawing of the nerve-net interface, spec information on microwire with a magnified cross-section. His eyebrows pushed together, faintly perplexed.

"When did this happen?" he asked. "Because I'm pretty sure I didn't register for the Atlantean upgrade program."

"Two years ago, a little more," Beckett told him. "Before you joined the SGC."

This merited a look up from the tablet.

"I died in Afghanistan, didn't I?" he asked.

"Brain-death," Carson confirmed. Radek glanced at McKay, who looked like he was remaining silent through pure force of will.

"Oh," Sheppard said. He tilted his head. "So all my memories -- "

"No, no no no, those are real," McKay said. Sheppard looked at him sharply. "Um. Ancient tech. Long story?"

"Are you all right?" Carson asked, leaning slightly to study Sheppard's face. He gave him an anxious, worried look.

"How come _they_ know?" Sheppard asked, indicating Radek and McKay.

"We wrote your code," Radek said softly. Sheppard's gaze returned to the tablet.

"You know, I've seen a lot of crazy stuff in this galaxy," he said, contemplatively, "but I'm pretty sure nobody will ever out-crazy Earth."

"Are you angry?" Radek asked, because he had to know.

"I don't really feel anger," Sheppard answered. His voice took on a distant, absent note. "I don't really feel a lot of stuff. Or dream."

He stood up, held up the tablet.

"Thanks," he said. "See you guys at breakfast."

And he left.

***

_This was how John Sheppard became the clockwork man:_

_An alien device of unknown origin, recovered by SGC, was attached to the temples of the subject and transferred his memories, via mystic unknown technology (this really annoyed McKay), to a small crystal in the centre of the device. The crystal was placed into an interface plate in the cybernetic brain, a hybrid of Earth, Ancient, and Alien technology, and it was carefully activated and sterilised._

_At least two years' worth of work was uploaded to the brain, to act as higher and lower reasoning functions, hormone regulation, decision-making, facial recognition, and a host of other functions the human brain performs without conscious notice. While this was proceeding there were multiple surgeries to implant reactive microwires all over the body to assist the nerves in conducting slightly-unfamiliar impulses from the new brain, as well as preserve the cohesion of the muscle and potentially improve reflex speed, strength, and healing time._

_The upload completed, several final tests for cohesion were run and, proving successful, the subject was wheeled in for one final surgery. McKay couldn't watch, and even Zelenka had difficulty as Carson removed the damaged brain matter and placed the shiny, well-protected cybernetic construct in its place before hooking the spinal cord and the microwire transmitters into its base. Cushioning fluid was added, the assisting surgeon closed up, and a second alien device healed the wound down to a sore scar on the back of his head._

***

Reading through it all, both the official reports and the unofficial musings, John really only wondered if they'd kept his brains. He'd kind of like to have them, he thought. In a jar on a bookshelf or something. Tastefully labeled "Two Heads Are better Than One".

Well, he thought it was funny.

He stayed up most of the night, puzzling out whatever he could about what they'd done to him, his left hand tucked between his head and the wall, fingers sliding back and forth across the narrow dent in the back of his skull that was all that remained of some pretty intense brain surgery.

In the morning he sat down next to McKay in the mess while Carson, across the table, was still trying to choke out a warning that the robot was coming. Zelenka was nowhere to be seen, but Zelenka wasn't one of nature's Morning People and preferred the ten-to-seven shift.

"So am I hooked into Skynet or anything?" he asked, and McKay froze with his coffee to his lips. There was a tense moment, even he could tell how tense (with his _big metal brain_ ), and then McKay wheeled on him, slamming the coffee down.

" _That's_ the best joke you can come up with?" he asked scathingly. " _Terminator?_ Seriously? You have all of Isaac Asimov and Philip K. Dick, you have _Blade Runner_ and several Star Trek franchises, not to mention Daleks and Cybermen. I can't believe you didn't go with Asimov. Asimov _invented_ the term robotics!"

John grinned around a mouthful of reconstituted egg. "I did consider some kind of joke about electric sheep. I thought Carson might take it personally."

Carson was still staring at the pair of them, open-mouthed.

"You aren't angry?" he asked. Sheppard felt a twinge, deep in some buried part of him, but nothing more.

"I can't get angry," he said.

"You're simulating it pretty well."

"That's not exactly my fault!"

"Mine," McKay said, holding a hand up. "Emotional subroutines are tricky. Faking facial expressions isn't."

"You don't feel at all...violated? I mean, McKay's been reading your mind for two years," Carson said. He jumped as McKay kicked him under the table.

"Feel free to feel violated for me, if you want," Sheppard answered, sipping his coffee. "I can't."

"It wasn't mind-reading. It was base code. And I haven't for almost nine months now."

"You're not at all worried that he's not more upset about this," Carson said to McKay. "You're not worried that he can't feel upset?"

"I'm not," Sheppard put in.

"Of course you're not, you ass!" Carson retorted. "You don't have the capacity!"

"Hey!" Sheppard said. "There's no need to insult me for having blinky Christmas lights in my head, you put them there." He paused, egg-laden fork halfway to his mouth, and tipped his head at Carson. Then he turned to McKay.

"So I wasn't brought to the research station on accident, was I?" he asked, as if the revelation was at hand. "I was sent there. I was supposed to sit in the chair."

"We...knew that you had the gene. We didn't know it was so strong," Carson said, tension making his voice high, doubling up his already considerable burr.

"Huh," John said thoughtfully. "Who else knows?"

"General O'Neill," McKay replied. Silence. "What?"

"General O'Neill?"

"He supervised," Carson said. "But just him."

"Oh, just," John drawled.

"What did you think, it was a conspiracy of physicists?" McKay asked.

"What about Elizabeth?"

McKay and Carson both looked horrified.

"O-kay. Seriously, nobody else knows?"

"This isn't the kind of thing that gets around. For god's sake, do you want me to win a Nobel for AI programming instead of real science?"

"I'm sorry, did you just call my brain fake science?" John asked.

And nothing really changed.

After all, they'd known for years what he was, and it wasn't like he had the ability to get very worked up over it.

***

"Aaaand finally," Sheppard held up a bit of paper close to the camera, so that it focused on a set of highlighted words: _Team Member Dex proved invaluable in treaty negotiations_. "This means, there's a planet in this galaxy that worships Ronon Dex as a god of just righteousness and things that go bang. Apparently it's the way he twirls his blaster."

Daniel, next to him, had a pencap between his teeth and was frantically scribbling down questions on a notepad.

"Dr. Jackson, if you're there, don't worry. I've flagged the report for you, and we'll be sending teams back soon. I'll make sure you get all the information earmarked."

"I love this guy," Daniel said around the cap.

"And now I have to kick you out, because I've got a couple of things to talk to General O'Neill about." On screen, Sheppard gave a little wave. Jack paused the tape, mid-wave, Sheppard's hand a blur, a tiny white scar standing out on his wrist. Daniel was already standing and muttering to himself, so Jack let him go and then once more disconnected the laptop from the screen and put his headphones in. He broke the pause; Sheppard finished his wave and sat staring at the camera for a few minutes, eyes showing nothing, face relaxed.

"So," he said finally. "I've had a word with the Doctors Demented about Tria Prima. They gave me the specs to look over. I can't say I understand most of them, but enough got through."

Jack forcibly unclenched his hands on the table.

"It's pretty weird," Sheppard said. "Objectively weird. But since my programming apparently doesn't extend to emotions a whole lot, it's not that weird for me. And I'm not really that guy, anyway, even if it were."

He looked like he was going to say something, then like he was changing his mind.

"I don't know why you picked me, or whether I was supposed to have some kind of significance," he continued. "But I'd like to buy you a beer for the whole saving-my-life thing, next time I'm in the area."

Jack smiled.

"That's all from Pegasus. Sheppard out."

***

_John decided he was okay with xenocide._

_Bang alongside it, as Carson would say. The Wraith made his life annoyingly full of near-death moments, both direct and through the terror-struck actions of the local populations. The Wraith threatened Atlantis and Elizabeth and McKay, so he was all right with wiping them out of existence. It wasn't anything personal. If they'd stop fucking feeding on human beings, he'd stop working out fun new ways to kill them in vast quantities. Maybe._

_McKay seemed to share his equitably amoral view of Pegasus race politics, but then McKay had removed his brain and put a computer in its place. McKay's priorities, while admirable, once again did not set a baseline for normal._

_Anyway, he decided to wipe the Wraith out of Pegasus and, if he only had dislike and a certain lack of conscience on his side, that would probably still be enough._

_Then John discovered the Replicators, and he found out how to hate again. Deep unpleasant uncomfortable gnawing hate, not an explosion but a slow burn, and as it built he unleashed it on his enemies like a gathered storm._

***

McKay was working, which was only natural for McKay, sitting near the wide glass observatory window in the mess with one of the lab's multitudinous laptops in front of him, a forgotten crust of a sandwich sitting on a plate nearby. John slumped into the chair across from him and waited, looking out at the late-evening stars, breathing soft in the otherwise-empty hall.

"Yes, what," McKay said, not looking up from the keyboard.

"I need to talk to you about being a robot," John said, and McKay's head whipped up so fast something cracked in his neck. "Don't concuss yourself."

"You want to shout a warning before you firebomb me like that?" McKay said irritably. "I thought we didn't talk about this."

" _Permission_ to talk about this, o great creator?" John drawled, and McKay flinched miserably. "I need to ask you about...programming."

McKay picked up the sandwich crust and gestured for him to continue.

"I get this...tape loop going in my head," Sheppard said, and this was something he had never done even before Afghanistan, before the neural net. "When I close my eyes. From...what they did."

McKay didn't quite meet his eyes. McKay was tortured; that could mean anything from sharp little knives and whirring blades to papercuts, given that it was McKay.

"That's what happens," he said.

"Not to me."

"Not even before?"

John shook his head. "Guys talked about it happening. I just...tried not to think about it. Seemed to work." He smiled, trying to lighten the mood, so that at least McKay wouldn't feel numb and awkward like he did. "Now I can't stop. The reel over and over. Getting home, losing the shields, blowing up Atlantis."

A real shudder ran through his muscles, but he kept his hands folded stiffly on the table. Losing Atlantis. Dying with Atlantis. And the overwhelming, orgasmic _rightness_ of it all, the feeling that dying for Atlantis was what he was made for.

Softer, a whisper under that, another memory looping intersected with the first.

 _Who the hell are you people?_ he'd asked.

 _They're not people_. McKay's voice was rich with fear and disgust. _They're machines._

"You need sleep," McKay was saying, and he jerked his head up, not realising it had dropped.

"How do I sleep?" he asked.

"Well, it generally _begins_ when you put your pyjamas on -- "

"No, _how_ ," John said. "How does that work?"

McKay chewed thoughtfully, set the last of the sandwich down, and began to talk.

He'd read the documentation on Tria Prima, but he understood mostly the mathematics, the variables, the basic physical functions. A lot of it was above him, not that he'd ever have admitted that to McKay. Still, in McKay's voice, under his mobile hands, it suddenly made sense. At one point McKay cupped his left hand and covered it with his right hand, forming an oblong space, smaller than he'd expected, representing the machine that now operated his body. The scale was undoubtedly precise. McKay would be nothing less.

He talked about compiling, downtime, buffer dumps, code corrections, cellular maintenance. His hands shaped the air into clips that connected brain to body, surgical pliers molding the microwires. John watched, fascinated, and listened.

"All of which means," McKay finished, "that this is something all of us have always had to deal with. Welcome to the club, Colonel."

He couldn't ask the question, you didn't ask questions like that, but McKay perhaps saw it in his face.

"Sleep a few nights straight through. It fades," he said.

"Can't you program it away?"

"It's not that simple, were you _not just listening to me_?" McKay asked. "I'm not talking to bask in my own genius, I don't have to talk to do that."

That was when the burn began, the realisation that the Replicators were like him except unlike, because their code was wrong, their imperatives were wrong, they were a cancer on existence, a parasite, a virus he wanted to hunt down and attack. They didn't even try to struggle against being machines, while he did nothing else. And if he destroyed them, Atlantis would be safe and maybe McKay wouldn't believe that machines pretending to be humans were wrong too.

Deep in John's neural nets, a new line of code wriggled into existence, something complicated to do with McKay and Replicators and tied up in the low-kindled rage. It surged an override on most of the other commands; it almost overtook the Executive Safety routine, the one that made him look sharply at anyone offworld who came too near Elizabeth.

_Protect Listen Protect Listen Protect Protect Protect_

"Well, glad we had this talk," John drawled, because that was expected. He stood, reaching for McKay's plate. As his hand closed around the rim, the radio in his ear crackled.

"Colonel Sheppard to the infirmary," Carson's voice, clinical but just a little worried. "Dr. McKay to the infirmary."

"On our way, Carson," John said, as McKay shut the laptop and tucked it under his arm. "What's going on?"

"It's Elizabeth. And the Replicators -- nanites -- you need to see this."

John broke into a run, and it felt like he didn't stop running until Elizabeth was awake again. Then he crashed, and slept for two days, and when he woke up the McKay Imperative had drifted into his code, lodged, and become immovable.

***

The instinct to protect Atlantis, overruling all else, was the only thing that allowed him to hand off his command to the Ancients when they returned. Atlantis sang under their hands the way it hadn't even under his, and they all stared at him as if they knew, as if they could see circuitry if they looked through the dilated pupils of his eyes. Obviously Atlantis would be safe with them, and that was what was important, wasn't it?

Sometimes the urge pushed wildly at him, on Earth, the urge to know Atlantis, to be sure she was safe. It was all that kept him in the SGC, a dog begging for scraps of information, doing tricks, leading teams through the gate. McKay's calls helped, and he saw Carson sometimes and that was good too, but an instinct to protect the city which he translated consciously into homesickness (for a city across the void, a planet in another galaxy) made him want to scream.

McKay flew in to have dinner with him and Carson (and Elizabeth, his fingers twitching with unrealised need when he saw her) and he picked McKay up from the helipad, took him back to his little military-issue apartment to change for dinner.

"I shopped," he said, by way of explanation, when McKay nudged a pile of books and DVDs on his kitchen counter.

"I see that," McKay replied, picking up _I, Robot_ (book, not movie -- even robots had some taste). He set it down and unearthed _Blade Runner_ , then set that on top of a hardbound second-hand copy of _Frankenstein_. "Gave up on _War and Peace_?"

"Well, I was looking for something meatier."

"You're missing _Ghost in the Shell_ ," McKay observed. And this was the nice thing about Rodney: he got to the really important shit. If John was going to read every book ever written on the philosophy of sentient robotics, on his way to a complete mental breakdown, Rodney wasn't going to stand in his way. He was going to make a required-viewing list. Probably with annotations regarding scientific accuracy and script quality.

He shifted aside a printout copy of Darwin Among The Machines and sniffed when he saw _The Matrix_ underneath, as if John had picked up pornography along with a copy of the Bible and some prayer beads.

"It's almost all fiction," he said.

"Do you know many nonfiction books about what it's like to live with a computer in your head?" John asked.

"Philosophy is Humanities."

"Why Rodney, you say Humanities like it's a dirty word."

***

It felt like they'd hardly returned, hardly finished repairing the damage done to Atlantis, when suddenly Carson Beckett was dead.

Rodney had known Carson for years. Inasmuch as he had a best friend on Atlantis (and John didn't count, that was...well, John didn't count in that way, that was all) it was Carson. Since they'd come to Pegasus Carson had patched his wounds, indulged his neuroses, shared his and Zelenka's pride over the success of Tria Prima --

And of course before Pegasus, before John Sheppard, Carson had spent twelve, fifteen hour days with them, working and reworking the plans, the three of them flying to Cheyenne Mountain from Antarctica to set up the medical suite. Weeks and then months on end they worked together, and months became years in Pegasus.

He wanted to communicate it to Carson's brothers and sisters, nieces and nephews and god, so many cousins. He wanted to make them understand that he and Zelenka and Carson had made this thing, two golden things: John Sheppard of Project Tria Prima, and Atlantis of Pegasus.

But he couldn't, because they weren't security cleared, and he wouldn't have had the words, and now he was back on Atlantis anyway. Pacing, sitting, working, pacing, the peace he'd found at the end of the pier completely shattered.

Sheppard was at the door.

"Atlantis thinks you're having a heart attack," he said without preamble. "She sent me."

"When you hear the voices in your head," Rodney replied, "do they tell you to kill people? Because there are drugs for that."

"You should know, you wrote them there."

Rodney sat, rubbed his face with his hands, looked up. "Did you need something?"

"I hear it, whenever it's quiet," Sheppard said, stepping inside, the doors closing behind him without his bothering to brush the access pad. "His voice, the infinite loop."

"Dump your buffers," Rodney replied ruthlessly.

"Do you hear him talking? Sometimes?"

Rodney looked up sharply. Sheppard's smile was thin and sardonic.

"I don't know how to make it go away," he said. "I just want to stop hearing him." He hesitated. "Yeah. So. I'm just gonna, go, and pretend I didn't say that. Sleep, right?"

Rodney reached out for him as he turned, hands cupping his head, holding him still -- Sheppard always led with his head, turning before his body did, leaning before he moved forward. Sheppard's eyes closed and he turned back, then turned slightly more, the edge of his mouth grazing Rodney's palm.

He didn't have a touch protocol, or at least he hadn't the last time Rodney was in his code, almost a year ago now, and he realised that Sheppard's body had been screaming for contact. He could see it in the way Sheppard turned his face into Rodney's palm, pushing against it, the way his hands came up to grab fistfuls of Rodney's shirt and then push into his chest because, _touch!_

The push stopped almost as soon as it had started and Sheppard pulled him instead, swaying but not staggering backwards as their bodies collided, his eyes opening.

"I want, I need, to know..." he said, eyes darting sidelong. "I hate and I hear him and I hate and -- "

"Colonel, stop," Rodney said, and Sheppard's head jerked forward, body stilling. "Hey, Sheppard's brain, meet hysteria."

Sheppard laughed at that, a short bark of amusement, but he let go of Rodney's shirt and smoothed it, tugging on the loose hem.

"You can't reprogram me?" he asked hopefully.

"Even if I could, I wouldn't. You're a person, and you're just going to have to cope with being a person the way the rest of us do. Do you get that?" Rodney snarled. "You're not my pet machine, you're not my brainchild, you're a person, you have your own memories and your own damages, and you write your own basecode the way we all do. I didn't program you. All I did was save your life, and you've amply repaid the favour."

Sheppard brought his arms up, knocked Rodney's hands away (ow!) and used his momentarily open stance to push forward, get them body-to-body again, jerked Rodney's chin up with one hand and kissed him.

"I need -- touch," he said, around the kiss. "I need -- you -- you can -- I can fix -- this -- if I have you -- "

Rodney made a mental note that if he ever got back into Sheppard's head he would see what brought this on, because there was no McKay Routine in Sheppard's head (Radek wouldn't let him put one in). Or there hadn't been, anyway.

"Please," John said, body jerking up and against and into Rodney's.

"I'm going to -- regret this," Rodney answered, as John licked into his mouth and then pressed his face to Rodney's throat. The world went still again, except for the push-rub of John's face against his throat.

"I can stop," John rasped. Rodney lifted a hand and tangled it in his hair.

"No you can't," he sighed. "Again, welcome to the club."

John laughed, a real laugh, which he'd never heard before, and resumed what was apparently a spirited attempt to crawl into his skin.

***

He'd had sex a grand total of once since coming to Atlantis. Since Afghanistan, really, and if he weren't a body housing a cybernetic brain he'd be more concerned that this was all some bizarre form of PTSD. He'd kissed an ascended Ancient and the princess of a degrading feudal court, and that had been all things decent, but he'd only had sex once, with Teer when he thought he'd be trapped away from Atlantis forever, and he hadn't really cared.

Since Afghanistan, it had been like rubbing away flaking skin from a sunburn or pulling a bandage off a healed wound, something to satisfy a bodily need, nothing more. No pleasure centers in the brain; orgasm was a thing he did, like brushing his teeth, a regular part of physical maintenance. Even that one night with Teer, he had enjoyed touching and Teer seemed to enjoy herself, but it was all sort of far-away.

John thought he remembered this, from his marriage, from being a teenager, from the few furtive mutual handjobs he'd had in Afghanistan. Real pleasure fired along every nerve and, though he couldn't help think of the microwires going into overdrive in his muscles, he was far too interested in getting Rodney's clothing off to care.

He straddled his hips, pinning Rodney to the bed. Even when he touched the hem of his own shirt it sparked senation in his fingertips, and pulling his shirt off with a stretch of arms felt better than most of the times he'd orgasmed in the past three years.

 _Cybersex_ , he thought randomly, feeling Rodney's cock rubbing against his trousers, and laughed again. He was here and half-naked and hard and this hadn't happened in -- years. Spontaneous desire, desperation. He wasn't even that interested in getting off, just wanted to touch and touch. He bent over Rodney again, trying to get contact anywhere he could, hands brushing his collarbone, his chest. Face pressed against his cheek because kissing wasn't enough. If he could bury himself here --

Rodney's fingers, which should be touching his back and shoulders and ass, were working away at the cold metal of his belt buckle instead and he hurried the process along, wanting skin skin skin. Thighs against his hips, trying to hold him in place, Rodney wrestling with him for who controlled this, setting the rhythm of their bodies pushing against each other and oh god, no sensation ever like his cock against Rodney's. This was better than coming home to Atlantis, better than the hot twisting hate of the Replicators, better than the day he woke up and the tape loop behind his eyes was gone.

He gasped and listened to Rodney murmuring, _easy, there, you'll sprain something, oh -- yes, not so easy now, okay_. Gasped, kissed him again, finally got his hands on his waist, pushed hard against his body. Over and over, chanting _fuck_ and _please_ and _I want_.

A little curl of code began to unravel, he could feel it in his mind, spinning out and overriding everything. It shed the Replicator-Hate and the _Protect Protect_ and strangled the Executive Routine and the Killswitch and the No Mercy Code and all his other functions, blacking out his brain, binary glowing white behind his eyes. Rodney gasped and he could feel a warm throb, Rodney's orgasm, and then his own from the crackling nerves everywhere they touched.

Air burned in his lungs when he stilled, clutching Rodney's hips, inhaling deeply as he rested his head on Rodney's shoulder. The new code flared bright and settled into the background, reintegrating. It left behind a gap where the over-and-over of Carson's last words used to be.

"It's gone," he said, and one of Rodney's hands left his skin briefly (no no no!) to stroke his hair. "I think you overwrote it."

"If only it was that easy for everyone," Rodney sighed, but he seemed pleased.

John shut his eyes and listened to the pulse of blood and the inhale-exhale of oxygen in both their bodies. He looked consciously for things he hadn't known existed, but the drumbeat of _Protect Listen Protect Protect Listen Protect_ had taken on a new shape, _Desire Please Protect Lust Listen Trust Touch Protect Listen Desire Trust Mine_ until he had to focus on the feeling of Rodney's skin under his lips to quiet it.

***

_John's twin competing urges were once Protect Atlantis and Protect Elizabeth. He'd never been torn between the two before; as a soldier it was his job to make sure the boss got out of the city if the city was going to disintegrate._

_A third desperate urge, after Carson's death, made him lean towards Rodney in the halls, lose his concentration if Rodney was too close. It brought John at night, loping along the quiet halls towards Rodney's quarters. It made him vulnerable to Rodney's suggestions, even when they carried with them the risk of losing Elizabeth or Atlantis or both. Sometimes you have to risk in order to protect._

_He hesitated too long when Elizabeth ordered him to abandon her, knowing that leaving her behind meant her almost certain death on the planet of the Replicators, where disgust and hatred made his skin crawl and his hands shake. But she ordered and his obedience was mandatory. He fought it, but Atlantis was the primary directive and Rodney was waiting for him in the Jumper. Save Elizabeth, lose Rodney and Atlantis; leave Elizabeth, battling his instincts every step, and save Atlantis and return to Rodney._

_This time when the Replicators took Elizabeth he ran the other way._


	3. Chapter 3

_...and sulfur represented the soul._

"You have to reprogram me."

Radek, alone in the lab, looked up sharply when he heard the voice; Sheppard was standing next to him, in that silent catlike way he had.

"We will put a collar on you with a bell, or perhaps with a little beeping thing," he replied. "Why reprogram?"

Sheppard's fists clenched at his sides. Radek looked down at them, and they eased open again.

"There's a protocol," he said. "I know, I can access it now. I can read my code."

"But not reprogram yourself?" Radek asked, intrigued in spite of himself.

"It's function-locked. It's about -- Dr. Weir."

Radek nodded. "The Executive Routine."

"I can't overwrite it."

"For good reason. It..." Radek spread his hands. "It is for the safety of the commander of Atlantis."

"Every minute I want to take a Jumper and go back there and rescue her, and there might not even be a her anymore," Sheppard said.

"Ah," Radek said, and felt a pang in his chest. "Colonel, what you are feeling, this is grief."

"Make it stop!"

"I cannot. It is natural, the way of things. It will fade."

"Now!"

"No." Radek frowned at him. "Is not right, and if you have come to ask me, this means McKay has already said no. McKay has told me many times, no more reprogramming, and I have agreed."

"Dammit, Radek!" Sheppard's fists clenched again.

"Hitting me will not bring Elizabeth Weir back," Radek said placidly, and he knew this because he had been very tempted to destroy something, even to hit McKay or Sheppard, when news came that she was dead, left to be cannibalised by the Replicators.

"It won't stop!"

"No, but in time it will only be every hour, and then every day, and then less on less. What would you have me do?" Radek asked. "Every time someone dies, I must go into your head and rewrite for you? What if I die and McKay dies? Better this way, to learn it once and know for the next time. You are capable of learning; we have hard proof of this."

"And what am I supposed to do until then?" Sheppard demanded.

"Grieve," Radek said. "There are books. Also there is work. Speak to those around you -- "

"Heightmeyer?" Sheppard drawled. "She's an ineffective diagnostic device, and let me tell you, I wasn't all that happy when I found that line in my code."

"Intriguing, but hardly topical," Radek said. "Many suggest one should write about it. Pluck," he said, touching his ear, "out of your head, put on paper -- in pixels. Busy yourself. Fight with your sticks. Be patient."

"Yeah, that's not really my strong suit."

"Well, now you must learn."

***

John Sheppard was a very efficient man, capable of multitasking and invigoratingly good at time-management. It was how he'd always had so much spare time to wander around Atlantis like a king, strolling into labs, talking to people in hallways, turning on that lovely, beautiful Charisma Circuit, which he always pictured as a little metal disc with three LEDs and a spiderweb of wires around it right in the middle of his brain.

_"What is this, John?" Teyla asked him._

He decided that if nobody was going to reprogram him, and he couldn't reprogram himself, he would take all of Zelenka's suggestions to heart. He would talk to someone, write about it, and keep himself busy, if not in that order.

_"It's a book," John answered, knowing that he looked sheepish, feeling a small spark of shame but mostly just the usual numbness, undercut with the ever-present urge to find Elizabeth, which was slowly fading as he got to know Sam Carter._

_"Any good?" Ronon inquired, looking at his own copy._

The anger started with the mission report, which he'd spent hours wrestling with, tapping out a few words, wandering away, coming back when he felt less homicidally inclined. This wasn't exaggeration; when he left the computer he would lean against the wall and think about getting both fingers around a Replicator's neck and squeezing. This was pretty irrational as a form of murder for a machine, so he upgraded it to shoving both of his hands directly into the Replicator's head and forcibly rewriting its code. But when the report was done he felt better. So, maybe it would work for other things.

_"You tell me," John said. "I sort of...wrote it."_

_"You wrote a book?" Ronon asked, amused and sort of impressed._

_Sometimes while he was writing or taking a break from writing he thought about Rodney. Rodney actually had rewritten the Replicator code, more than once. He thought it was pretty amusing that everyone thought he was the ruthless one, when Rodney was the guy who basically brainwashed an entire race to throw themselves into battle against the Wraith. Rodney didn't lose sleep over it, either, not until the Replicators began killing humans._

_Teyla traced her fingers over the plain printed cover. It had cost him to get it printed and bound, and he'd had to go through O'Neill and a military publisher. "Is it a story?" she asked, meaning, was it fiction. In the Pegasus galaxy sometimes fiction and reality got a little mixed up._

_"It's about me," he said. "And partly about some other stuff, too. I thought you should know, that's all."_

Sometimes when he thought about it he hunted up Rodney and unspun his code under Rodney's hands until the binary pushed him over the edge, seeking reassurance that he wasn't the machine, he was John, and Rodney didn't hate him.

_Ronon came up to him the next day. "I finished it. I want to translate it into Satedan. Lemme do it."_

_"Why?" John asked._

_"It's an epic," Ronon answered. "It's a warrior's story. There were lots of books like this on Sateda. Well, maybe not exactly like this."_

_"I have to ask McKay and Zelenka," John said, feeling a surge of something, washing over the numbness, for Ronon and all the burned books and the dead on Sateda. He suspected he would have really liked Sateda before the Wraith._

When he was finished he didn't give proofs to McKay or Zelenka to look over, because it wasn't technically a spec manual for his brain. It was what he'd want to have read if they'd told him at the start what he was -- it was the talking-to-people part of Zelenka's prescription. It was about him and _Frankenstein_ and Rodney McKay and Isaac Asimov and Carson Beckett and Radek Zelenka and _Do Androids Dream Of Electric Sheep_ and Elizabeth Weir and C-3P0 and Jack O'Neill with maybe a few disparaging remarks about the Butlerian Jihad thrown in for good measure.

_"This -- what was done to you -- is not common practice on Earth," Teyla had said, when she finished it a day after Ronon._

_"I'm the only one," Sheppard answered._

_Teyla slid her hands up his arms and bent forward invitingly and he touched his forehead to hers._

_Oh, he thought. I remember this. This is joy._

There were charts and diagrams too, but he'd redone them all so that they made sense to him.

_"You did what?" McKay asked, looking at the book as if it might bite him._

_"It's probably not very good," John said, setting it on the table._

_"And breaks about eight million confidentiality agreements we all had to sign!"_

_"I didn't have to sign anything," John replied. He glanced at Rodney and grinned. "I say nice things about you in it."_

_"Well, you'll probably have gotten all the cybernetics wrong," Rodney muttered, but he picked up the book and started to read and when John came back a few hours later both he and Zelenka were speeding through it, totally ignorant of his presence._

The slim book was titled _The Modern Prometheus_ (why mess with a good thing?) and on the author page it listed Lt. Colonel John Sheppard, Dr. Carson Beckett, Dr. Rodney McKay, Dr. Radek Zelenka. Rodney predictably bitched about third-place billing, but he did it while John was curled around him, skin on skin as close as possible, so John ignored him and thought about how beautiful and elegant his base code was instead.

_"How's the translation going?" he asked Ronon, who offered him a paper notebook filled with words he couldn't read._

_"I'm leaving out the science-y parts," Ronon told him._

He had meant to collect the books up again and burn them when they were done reading them; after all, he had the PDF if it was ever needed. The books were just to explain to Teyla and Ronon how he felt, really, and as a present to Rodney and Radek. Instead, with John's permission, Rodney gave a copy to Samatha Carter, who "forgot" to ask permission before giving it to Lorne, who circulated it among the Marines -- trusted ones, Pegasus veterans -- who passed it on to their pals, who mentioned it to the scientists, who stole Zelenka's copy. Zelenka furiously demanded a replacement, so John went and intimidated the book back from Miko and gave her the damn PDF and said they could all go to hell. Miko gave it to Dr. Keller, who put it on the shared medical server.

_He expected suspicion and fear and maybe even pity; certainly he expected curiousity from the scientists, but instead the ranks closed around him and the scientists pretty much ignored him like always. The few Marines who said they didn't want a robot leading them into battle never got close enough to the Colonel to express their sentiments, what with being in the infirmary and all._

_The worst it got was Lorne at mess asking, "Hey, so can you shoot lasers out of your eyes?" and winning almost three hundred dollars off of various Marines when McKay looked up from his meal and said, "Why is it always lasers? What is it with you people? He can't shoot lasers out his eyes or his ass or any other part of his anatomy. Go fondle your sidearm."_

General O'Neill found out and, while John was still on Earth after being recalled to _oh yeah rescue McKay's baby sister, thanks, Rodney_ , he gave him a twenty-minute dressing-down about confidentiality in the military, which left him skinned and hollow. Dr. Jackson, catching him in the hallway afterwards, offered him a printout of his PDF annotated in red pen, a worn copy of _The Tin Woodman Of Oz_ , and a slightly awkward, slightly absent grin.

_In the SGC compound, out of his hearing, they murmured about the machine man. He fed a man to the Wraith, they said. He didn't even look unhappy about it._

_"Well, he's not like us," one of the Marines said, as if that explained anything. "Computers don't have feelings."_

***

It was true, sometimes. Others, not so much.

They found Elizabeth again, only she wasn't Elizabeth, only his stupid _base code_ didn't know that.

And they also found...him. Himself and Teyla and Ronon and Rodney. He wanted to ask his other self if he knew whether or not he had a cybernetic brain, if maybe the Replicators had built him a new human brain, but that was a little too Pinocchio for his tastes. _Are you a real boy?_

It was easier to let Elizabeth go the second time; he'd had months to imprint on Sam Carter as his mission commander and her rule overrode Elizabeth's. Still, he felt pain and loss and impatience and fear as Elizabeth abandoned him again.

After that, back at Atlantis, John threw himself into work. Any spare minute that he didn't know what to do with, he worked hard. He was grateful to Radek for this, at least: he knew now how to grieve. He did paperwork, he drilled the Marines, he worked on the book. Once he'd added Dr. Jackson's annotations and fixed some grammar, he spent hours staring at the document.

Finally, he added a frontispiece:

_Remember, I am not recording the vision of a madman. The sun does not more certainly shine in the heavens than that which I now affirm is true. Some miracle might have produced it, yet the stages of the discovery were distinct and probable._  
\-- Mary Shelley, _Frankenstein_

_You aren't my pet machine or my brainchild. You're a person, damaged like we all are, and you have to rewrite your own code the same way we all do._  
\-- Dr. M. Rodney McKay

Then he tabbed to the end, inserted a page, and began work again on a new chapter.

_Epilogue: Dr. Elizabeth Weir_

_There are certain lines of code that are function-locked away from me, but that's true of anyone. I can't stop breathing and I can't stop my heart from beating any more than any other person can. I was programmed to protect the next place I would be stationed, which I have done like a soldier should. I was also given an Executive Routine, an imperative to protect my mission commander at that station._

_Technically the Executive Routine allowed me to accept any person fulfilling her position, but I imprinted early on Dr. Elizabeth Weir. Dr. Weir was a diplomat and scientist, and my direct superior for three years following my return from Afghanistan..._

***

_Destroying the Replicator planet made him so high that he just sat in the workout room, legs pulled up to his chest, head on knees, and flew and flew and flew._

_It wasn't until he came down that he realised there was an empty aching place where the hate used to be_.

***

"This is so cool," McKay said, holding the bullet up.

He was lying on John's bed, shoes off, rumpled trousers and shirt testament to the fact that McKay had mastered "laundry" but not "folding". John looked up from the desk, looked over at him, frowned.

"Well, yeah, who doesn't love getting shot offworld?" he said, pecking out an email with his single functioning hand.

"Yes yes, heart in my throat, pulse fluttering, visions of myself weeping over your lifeless body passing before my eyes," McKay said, still studying the way the bullet caught the late-afternoon sun through the window.

It looked a little like a dime that had gone through the garbage disposal. It was still vaguely bullet-shaped, but there were gashes across the metal and missing chunks too large to be explained by ballistic scars (or impact with his shoulder). He adjusted the sling immobilising his left arm, fingers twitching at the memory. The surgery had gone well and he was perfectly fine, but he hated not being able to use his hand.

"Did you ever consider the fact that my components were going to wear out?" he asked McKay, who rolled his eyes.

"Your brain is composed predominantly of alien alloys and parts -- "

"Great, so I'm an alien robot."

"My heart bleeds for you. Returning to the point, we had no idea how long your parts would last, but it was a good bet we wouldn't have to worry about buying the extra-long warrantee coverage, metaphorically. And self-diagnostics would have made you contact the parallel program on the server and notify us."

"My brain would email you."

"Gross simplification, but yes. Instead..." McKay twirled the bullet across his fingers. "Your brain has begun to heal itself, when and how it can. It explains why you've been craving certain foods. Your brain is sending impulses to your body to intake minerals, even trace amounts, transport them via the bloodstream, and incorporate them into minor repairs as needed. When it got a big hunk of metal at once, it started ripping out anything it could get to before Keller removed it."

"This is all very creepy," John observed.

"I thought you'd come to terms with your inherent creepiness," McKay replied.

"I would, but every time I do, new creepy pops up," John said, moving to the bed, easing himself down into a sitting position. McKay, who perhaps had been a little conditioned by now to what John wanted, rolled to the side and curled around him, knees tucking up against his thigh. McKay held up the bullet and John took it, rubbing his thumb across the rough cannibalised metal before setting it on the side-table with a soft _click_.

"What happened to you is an open secret at Cheyenne Mountain now," McKay said, looking more serious. "I'm surprised there hasn't been a call to have you replaced."

"There has," John said before he thought about it.

"What?"

"Caldwell."

"See, I don't get why he even wants this job. Is he really that eager to get, I don't know, turned into a bug or stranded in fucking _Middle Earth_ for six months or -- "

John pressed his thumb to McKay's mouth. He'd tried, a few times, just telling him to shut up; except on missions, it never did any good. This was the easiest way.

"Caldwell brought it up to the IOA. O'Neill found out and said that if I was recalled because of Tria Prima he'd resign, and Dr. Jackson said if O'Neill went, he'd go, and Carter got hold of that and told the SGC that she wouldn't support any replacement that was sent and she didn't think the Marines would either, and got Lorne to back her up. Lorne threatened to sic you on them. I think really that's what did it," John mused, easing his thumb away.

"You didn't tell me," McKay accused.

"I didn't see you. By the time I heard about Caldwell, everything was already happening. It was over in a few hours. Must've been a fun afternoon at Cheyenne Mountain. I really owe those guys a beer," he mused.

"You could have told me after."

"I've got the emails, if you're interested. Dr. Jackson BCC'd me on everything."

"Spare me the wank of soldiers and scientists," McKay replied. "TL;DR."

"Yeah." John pushed his shoulder with his good hand, but McKay nudged him with a knee and didn't roll. Instead he slid back and let John lie down, then curled around and over him, nuzzling his face into John's neck. His hands skidded his shirt up, and the familiar _Want Lust Listen Protect Mine_ kicked all other thought out of his head.

***

He didn't feel much when his father died. He'd never built code for anything even remotely connected to love, when it came to his family, not that he'd had a whole lot even before.

What he wanted to say to his brother was, _Do you think he would have been happier if I'd died in Afghanistan?_

No, what he wanted to say was, _You didn't have to stay either, but I'm not the prodigal son. You have to come back while they're still alive to be the prodigal son._

Actually, really, what he wanted to say was, _I'm sorry, Davey_.

Maybe what he wanted to say was, _I'm not like you anymore._

Really, okay, what he wanted was for his father to be alive, and he wanted to say to him, _I have seen what you couldn't imagine. Do you know what it's like to fly? Do you really get how it feels to have speed and distance and space to move in? Have you ever seen the mountains in Antarctica? Do you know that I have a computer instead of a brain in my head, and I'm sleeping with the man who put it there? Do you want to meet Rodney, Dad? He saved my life and I wrote myself a computer program just so I could be in love with him._

_I've seen men who feed through their hands. I've seen a planet implode. I've lived in a floating city and I've made her fly. I've traveled across the void between galaxies. I've deposed kings and dictators. I speak the language of a race that's no longer alive._

_Do you see, Dad? Do you understand what I've seen? Do you understand who I am? Do you get that I'm not the disappointment, that while I could have been a junior VP in an office building I chose to risk my life for a planet that's not even my home anymore? Do you **see?**_

Just as well he was dead, 'cause saying all that would have gotten him in so much trouble with the IOA.

He ended up with a day to kill on Earth, before he and a handful of new arrivals were scheduled to ship back to Atlantis, and he finally managed to buy General O'Neill and Dr. Jackson their beers. Dr. Jackson sat across from him with a small paper pad, taking hasty notes while he asked question after question about the worlds he'd visited and the people on them. He bought the second round to make up for all the questions, and of course O'Neill insisted on buying the third round.

Jackson leaned forward, notebook set aside now, restless eyes shifting first to O'Neill at the bar and then back to Sheppard.

"Tell me about Atlantis," he said.

"It's great," John answered. "You've read the mission reports."

"Yeah, but that's..." Jackson made an unsatisfied noise. He was another like McKay, constantly curious, picking at threads to see where they'd lead. Unlike McKay in any other way -- abstracted, well-mannered, and of course his curiousity was for history and people, not for the future and the stars. Still, something inside him twisted with the familiarity of it all, and he found that he actually _liked_ Jackson.

"Do you miss it?" Jackson pressed.

"Her," John answered.

"Huh?"

"I miss _her_." He made a face -- reluctance, confusion, lips pressed together, trying to put it to words. Before he managed it, Jackson nodded.

"Oh," he said. "It's that way."

"Yeah."

***

That year he saw a lot of Earth, more so than usual for life in Pegasus. It used to be that a return to Earth was only for dire emergencies but, these days, he occasionally got called back to Cheyenne Mountain for a few days just so some IOA bigwig could have a face-to-face with the Colonel. This wasn't all bad; he could load up on junk food from Earth which was good barter in Atlantis' still largely trade-based economy. So, when he saw the email notification that he was scheduled for a quick trip across the bridge in a couple of days, not too long after visiting for his father's funeral, he didn't really pay much attention.

Rodney, on the other hand, swore in three languages when he saw his name and Zelenka's on the manifest, shoved someone away from the nearest computer in the gateroom, and checked the infodump they'd just had from weekly dial-in. Then he looked up at John, who looked back at him with amused expectance.

"Who'd you piss off at SGC?" he asked, leaning over his shoulder, keeping his voice low.

"Nobody," Rodney said. "Well, lots of people, but nobody especially badly. They're calling us back to assess Tria Prima. Your five years are up."

John blinked. "You make it sound like they're going to execute me."

If Rodney intended the look of cold, naked fear to reassure him, he'd miscalculated.

"They're _not_ going to execute me, are they?" he asked.

"Not intentionally," Rodney answered, still staring at the screen.

"Rodney -- "

"Not here," he said, closing the laptop and walking away. John ran to catch up with him in the corridor.

"Hey, what the hell?" he asked, trying to dodge around people in the hallway, keep up with Rodney's pace, and turn to face him at the same time. "You're freaking out, Rodney."

He managed to drag him off course, into a side-hall that wasn't often used, and kept hold of his arm as they faced each other.

"So they ask me a bunch of questions, I'll give them the book, big deal," he said under his breath.

"This isn't some post-traumatic stress evaluation," Rodney answered. "The final analysis of Tria Prima -- " he looked aside, haplessly. "Did you read that far in the proposal?"

He hadn't actually read the grant proposal for the project at all, just the specs for installation and the medical reports.

"We have to go into your head again. Physically," Rodney said. "Investigate how the circuitry's functioning. And all your code." He gave John a mirthless smile.

"But that's not going to kill me," John answered, uncertain.

"It's not exactly a papercut, so excuse me if I'm not comfortable with them scooping your brain out of your head again," Rodney hissed. "Besides, it's not that simple to get into your code anymore. It's organic, it's probably incredibly disorganised because you're a _crazy person_ , and -- "

"And they're going to see my code about you, huh?" he asked. Rodney stared at him, stunned.

"You have code about me?" he asked.

Oh. Maybe that hadn't been where he was going with this.

"Listen, Rodney, I can get out of this. They can't order me to have brain surgery. There must have been some kind of...listen, did they think...they can't just switch me off," he said lamely.

Rodney looked down. "Oh, and also, we could totally reprogram you. You know. Take out Elizabeth and -- other things. Like you wanted."

John felt his fingers clench and forced himself to let go of Rodney's arm so that he wouldn't bruise him.

"Take you out?" he asked. "Is that what you think I want?"

Rodney looked miserable. "I don't know what you want. I -- we didn't think this far ahead when we started. We certainly didn't think we'd be in another galaxy when we finished."

"Is there anyone you'd trust to do the surgery?" he asked. "Anyone here or on Earth?"

"I can look up the attendings Carson used -- " Rodney shook his head. "Keller's the only one I'd trust to know how important this is, and she's not exactly the world's greatest surgeon."

"But once this is done, that's it, right? It becomes someone else's problem, I'm just the test subject." John let his head drop slightly, almost forming the Athosian gesture. He was thinking, surprisingly for the first time, of the guys he'd known in combat. Some of them went home hooked up to a respirator, and their eyes weren't ever going to open. Not like his had. "When this is done -- "

"Phase II. Multiple human trials," Rodney's voice was almost a whisper.

"Other people getting tin brains?"

"It's not -- "

"I know." He drew a deep breath. "If it hadn't been for Tria Prima I wouldn't be alive. I kinda owe the project to see it through. Back on Earth we could be fixing people like me."

"They could break your brain."

"They're not gonna break my brain, Rodney."

Rodney, to his surprise, butted against his chest with his head, forehead just below his collarbone. It was weird and intimate and not something he wanted to do or have done to him in a public place, but he just let him do it and kept an eye out for anyone wandering the halls.

"Of course you're not frightened," Rodney said, finally, with a sigh, and stepped back.

"I can't help it," John muttered.

***

"No, no, and no, you idiots," Rodney said, and the room fell quiet around him. "You can't use general anaesthesia on someone who hasn't got a chemical brain. Christ, I'm a doctor of Physics and I know that."

"But all reasonable indications -- " one of the others at the conference table said, and Rodney snarled back.

"Would you really like to base the success of Tria Prima on reasonable indications? Hell, let's flip a coin! I'll call tails, since _reasonable indication_ has shown it comes up five percent more often." He rubbed his forehead. "There's no way of knowing how it would affect the neural net. Just because he's had hallucinations and virally-induced reactions in the past doesn't mean it's safe."

The august assembly of medical professionals and cybernetics specialists seated in the tiny, cave-dim room under Cheyenne Mountain had grown progressively more combative as they discussed the surgical procedure. Sheppard, sitting in a corner, had gotten quieter, withdrawing further into the shadows, until finally Rodney had made the executive decision to shout them all the hell down.

"I am the project manager of Tria Prima and unless you really want to have General O'Neill come in and mediate this you are going to have to go through me."

"And me," Zelenka added, without looking up from the tablet he was retrofitting to interface directly with the cybernetic brain.

"Yes, of course," Rodney said irritably. "You," he added, pointing at Doctor Whateverhernamewas, "We can do this with local, it'll be a matter of timing. Last time it didn't matter what we used because his brain had effectively been switched off, and oh yeah, guess what, we're going to switch it off again."

"Are you certain you won't -- " Doctor Bigmoustache began.

"How simple do I have to make this?" Rodney said wearily. "We can uplink wirelessly from the tablet to the brain. As soon as we're certain we have a secure connection we can switch off the pain-receptor circuitry. Zelenka and I will document our coding while you voodoomen shake your bone saws and very, _very_ carefully engage in the physical examination of the -- "

He broke off, because Sheppard was standing up; he shot him a questioning look and got a bland, blank smile in reply.

"Just getting some air," Sheppard said, picking his way through the mess of chairs and scientists. Rodney watched him leave, faint anxiety flitting through his head, but then Doctor Annoyingquestions took this as an invitation to speak without being spoken to, and Rodney had to slap him down.

***

It wasn't like you could ask Dad for the keys and take an F-15 out for a spin, but John's high security clearance and command of Atlantis did net him a few perks, one of which was immediate access to the base helicopters and a pilot to fly him somewhere if he wanted.

He did not want. He borrowed a flight suit, ran through preflight with his pilot, then kicked him out on the tarmac and took the yoke himself.

Right around four thousand feet, his head started to clear.

He'd been accustomed to the occasional strange look in Atlantis, and Lorne's good-natured one-offs about laser eyes or tin soldiers. None of the doctors here were hostile at all, either, but they were curious and rude. Which in McKay was a sign of genius and also not half as annoying as you'd think, but in these people made him feel like he couldn't quite connect to his own body. They looked at him and thought _robot-brain microwires neural-net charisma-circuit what-do-you-think-would-happen-if-we-poked-him-with-sticks?_

And they made McKay think that way too. There was no other way to say "I'm going to set this computer up to talk to your cybernetic brain", of course, but McKay didn't seem to think he cared, either, wanted him in the room for these discussions. He was nervous enough about them taking the top of his head off.

Nobody was ever going to award John Sheppard for outstanding introspection or mental well-adjustment (and if he wanted to be well-adjusted he'd need one of those tiny screwdrivers, hahaha). He'd be the first to admit that even before three mad scientists transplanted his brain he hadn't been that great a guy. But nobody on the outside ever looked at him and thought, not a person.

McKay had never treated him as anything less than a person. Until now.

His radio crackled, and then a familiar voice came on.

"Colonel, you are the only asshole I know that chooses to sulk in low geosynchronous orbit."

"General O'Neill," he replied.

"Get your butt back down here, son."

"Copy," he said, and regretfully turned the chopper back towards base.

When he was through with postflight and wearing his own clothes again, he slouched and dawdled towards O'Neill's office, aware that whatever he'd done he was probably in trouble. O'Neill was leaning back in his chair, studying a file folder.

"Have a seat," he said, gesturing to the other chair. When John sat, he tossed the file across the table at him.

Inside were a handful of small photographs, dwarfed by the large manila spread of the folder. A guy sitting on a rock with an enormous dog at his feet; a woman holding Fourth-of-July sparklers; a random, awkwardly-posed family portrait; a young boy.

"Just in case you're losing perspective," he said, as John turned each one over. The guy with the dog was an Air Force Captain; the woman was an Army Sergeant; someone in the family portrait was a Marine Corporal; the boy didn't have a name.

"Those three are on life support in Cheyenne Mountain, awaiting a procedure I think you're familiar with," O'Neill said, voice low and dangerous. "If they don't get help, they'll stay that way for the rest of their lives. If they do, they could be up and around in a couple of weeks."

John nodded, wondering if he was supposed to be feeling guilty.

"Who's this?" he asked, flicking the photograph of the boy up between two fingers.

"My son." O'Neill said, face carefully blank. "Accident when he was nine. He shot himself. Unlike them, it's too late for him."

"I'm sorry," John murmured, and was startled to discover that he was. It hurt Jack O'Neill, obviously, it would hurt anyone. John could share in that hurt, at least. He tucked the photographs back into the folder.

"I think Dr. McKay has shouted everyone into submission," O'Neill said, avoiding his eyes as he took the photos back.

"I should make sure he doesn't bite anyone during dinner," John sighed. He was at the door before it occurred to him, the enormity of what O'Neill had just casually done. He stopped, though he didn't turn around. "Thank you, General."

"See you post-surgery, Colonel."

***

Three days later he was seated in some bastard form of dentist's chair, sterile and swathed, surrounded by medical equipment and doctors. In one corner of the room there was a tented-off area, clear plastic curtains protecting a desk with two laptops and a tablet on it. He could see Rodney and Zelenka in scrubs and thin latex gloves, already tapping out commands.

"We're going to do this nice and easy," the lead surgeon said, face already blocked away behind a mask. "How are the restraints?"

John flexed his fingers. The straps holding his wrists and ankles were tight enough that he couldn't even flex much, let alone pull away. He felt like he was about to be executed after all. The strap holding his head in place was itching against his forehead.

"Fine," he said.

"All right. You'll feel a series of pinpricks, that's the local. As soon as we've established it's in effect, we'll signal to Dr. McKay -- "

"I know the procedure," John replied impatiently.

"Let's get started, then," the doctor said, gesturing for one of the nurses to bring a tray of instruments forward.

John closed his eyes, tried not to struggle against the restraints, and hoped like hell Rodney would turn everything off quickly.

***

"Taking down higher cognitive functions," Rodney said, brushing a knuckle against his cheek to move his mic closer to his mouth. "Pain receptors are...out."

There was a buzz from the general area of the surgery table.

"Not yet! Jesus, give me ten seconds to make sure before you go cutting his head open, okay?" he studied the readouts, more to make his point than anything, and finally nodded. "Okay. He's unconscious. Pain centers are down, only the basic subroutines are online and we are...receiving information. Uplink's fine here. Now you can go."

He tried to ignore the coppery smell of blood over the antiseptic and the burr of saw on bone as he watched the data flow. The uplink was dumping the old code first, the stuff that was easier to sort out because it had never been rewritten or incorporated into active operating code. Breathing, heart-rate, all the good stuff that had been such a pain in his ass and Zelenka's when they were writing it.

"Ah, I have so much nostalgia," Zelenka said, grinning at him from the other laptop.

"Mm, I prefer not to remember spending fifteen hours a day on code," Rodney answered. He tried not to look at what they were doing to John's body, strapped into the chair. The night before, after the final cold-run and the last evening debriefing, he'd gone to the room they'd assigned John in the crew quarters of SGC and found it locked -- they'd hardly seen each other since they arrived, except in meetings, and even then John wasn't fully...there, was checked out to some inner world.

The scrolling code grew more complex in front of his eyes, subdividing and diverting, cross-referencing itself, John's conscious thought patterns beginning to emerge. Zelenka, at the other computer, was studying his facial-recognition routines.

With the potential exception of Carson, may he rest in peace, none of the leaders of Tria Prima had actually been interested in the practical application of the AI software. It had been a challenge, an intellectual puzzle, an experiment -- like seeing how high you could build a tower out of blocks before it tumbled. Of course it was nice they were going to be able to help people and all, but that wasn't the point. The program was an end in itself, and the result was --

Rodney narrowed his eyes at the computer screen, flicking back several lines. Here, everything was organic and jumbled, like trying to read stream-of-consciousness, but he could see familiar things -- a touch protocol, an emotional reaction, an override on all but the most basic imperatives. And his name, over and over again in the code.

Then the screen flickered, briefly, and Zelenka swore, and the doctors began shouting.

"Oh my god," one of them said. "Dr. McKay! Dr. McKay, he's -- "

"Waking up," McKay breathed. "Shit, no, nononono, Zelenka, his cognitive functions are coming back online!"

Zelenka was already typing, swearing under his breath in Czech, trying to shut down the neural net, but every circuit on the board was lighting up and when he raised his head John's eyes were open. Some basic self-preservation instinct John had written into his code --

The pain receptors flashed back online. John began to scream.

"Shit shit shit shit shit," Rodney chanted, trying to close down the self-preservation code that was making John's arms tense, his heels drum against the chair in a stacatto beat.

"We have to shut it down!" Zelenka called.

"We don't know what -- "

"Rodney, we must cold-start!"

"Okay, no, wait -- it'll dump -- _Jesus_ ," Rodney swore, as John's screaming went on. "Download it. Download it all. Back it up, Radek!"

He bolted from the desk, shoving the doctors out of the way and grasping John's hands on either side of the chair.

"Colonel, Colonel, look at me, we're going to shut you down -- "

"Thirty seconds!" Zelenka called.

"Come on, John, hold on for thirty seconds, if we don't get you all into the computer -- "

"Dr. McKay," one of the doctors said.

"Shut up," Rodney snarled, fingers fumbling for John's. His eyes were rolling back in his head and he was struggling, straining against the straps.

"Fifteen seconds!"

"Fifteen seconds, John, look at me, _look at me_."

"Cardiac arrest," one of the nurses called, right as Zelenka shouted "Done!" and there was a very loud click, and John's eyes closed. The screaming stopped but the dead, ringing silence wasn't any better.

"Get him on a respirator, his brain's not telling his body to breathe," Rodney said, moving out of the way so they could move in with the defib machine. "Zelenka, what the hell happened?"

"Busy!" Zelenka called, and Rodney bolted back to the laptops. "Look, here is what I do, remove consciousness, basic code only, re-upload -- "

"Do it," Rodney said.

"Rodney -- "

"Clear his memory and do it! We have the backup!"

Zelenka's hands moved eerily fast over the keyboard, dumping all the complex, beautiful code out of his memory and replacing it with something new, a basic algorithm that let him breathe and keep a pulse and that was about all.

While the doctors were still trying to jumpstart John's heart, he opened his eyes and inhaled and sat very, very still.

Rodney lowered his head and rested it on his folded arms, trying not to break down.

"Dr. McKay?" one of them asked.

"Keep going. We might have just killed him. We'd better make it count," he said, in a voice that was not as steady as he would like.

"No file corruption," Zelenka offered. "His memories are untouched. His operating code, I have it on this hard drive. He will be fine, Rodney. We will upload when it is finished."

"We just downloaded John Sheppard to a Dell. Give me a minute, okay?" Rodney said shakily. Zelenka watched, all anticipation and curious eyes, until he pulled himself together and sat up.

"Send it to me," he said dully.

"Are you certain -- "

"Radek. Send me his damn code," he said, and a few seconds later it started scrolling past again. "We need to document it."

"You could go sit with him," Zelenka said quietly.

"He's not out there. He's here," he replied.

***

Jack stood in front of the man lying in the intensive-care bed, a thin pink line all that was left of the surgery the day before.

"How are you, John?" he asked.

"Systems functioning," John said. He didn't open his eyes, and his voice had an odd toneless quality to it, not quite metallic but not quite human.

"See, now that's what I thought he'd be like when you suggested this," he said to McKay, who was seated at the bedside, working.

"General, I say this with all due respect, if you are going to be an asshole you can leave," McKay replied. Jack blinked at him, then smiled a little.

"Well, it was that or tell you I have faith in your genius, and you don't need to be told that," he replied. "What's the holdup?"

"I'm sorry, I'm about to upload a man's entire personality after we dumped his buffers, excuse me for wanting to ensure that it's going to function properly before I bother," McKay snapped.

"I prefer Sendspace," Jack offered. McKay snorted and tapped one last button on his tablet, circling around and setting it next to Sheppard's legs on the bed.

"John," he said, with a gentleness Jack hadn't been aware McKay could possess. "I'm going to start the upload now."

"Acknowledged."

McKay flinched at the single, uninflected word.

"It'll incorporate as it uploads," he said, talking to the tablet but apparently addressing Jack. "He should start to...if it works, he'll be disoriented for about five minutes. Then he should be fine."

Jack watched, interested, as McKay started the uplink. The good doctor didn't seem to know what to do with his hands; they hovered above the screen, then touched the blanket lightly, skipping over the hospital-grade wool, drawing back every time his fingers made contact.

Sheppard's eyes opened and, for a moment, he simply stared at the ceiling. Another moment; he swallowed and opened his mouth. Jack wondered if he should fade back, not witness whatever the Colonel was going through -- but after all, Tria Prima belonged to Jack O'Neill as well.

"McKay," Sheppard rasped, turning his head.

"Hi, John," McKay said quietly.

"I don't know what you did," Sheppard said slowly, "but I can't move my fingers."

"You were cold-started," McKay grinned. "We had to control-alt-delete your uppity ass. Give it a minute or two, you're still running system checks."

"Oh," Sheppard mumbled. "General," he added, with a nod. "Scuse me if I don't salute."

"In your own time, Colonel."

Sheppard looked down at his hands, fingers finally twitching, and lifted an unsteady arm to lay his palm across the tablet.

"This is weird," he said slowly. He walked his fingers across the tablet's case to McKay's wrist, uncoordinated muscles clenching as he gripped it.

"Give it a few minutes," McKay replied. Sheppard sucked in a breath sharply. "What?"

"Just -- new code coming online. Old code. Coming back," he said, and Jack watched as he turned back to McKay and stared intensely at him.

Well. So along with reasoning and bodily functions and higher cognitive skills, a man with a clockwork brain could be programmed to love. Good to know.

"I'll want your report this afternoon, McKay," he said, but neither of them even acknowledged him as he slipped out.


	4. Epilogue

**Alchemy:**   
_The early study of science, combining chemistry, metallurgy,  
 _physics, medicine, and mysticism in the search for revelation.__

The databurst from Earth came in the early afternoon, local time, and carried with it an entire packet of documentation on Tria Prima. Doctors at Cheyenne Mountain had taken over the study, a smooth if somewhat intense handoff (Rodney McKay was nothing if not intense) once John was capable of returning to Atlantis. The surgery had taken its toll on his body, which still twinged a little in the mornings all these weeks later, and the cold-start had given him an odd sense of disconnect that only began to fade when he was back -- back home, back in Atlantis where he'd learned how to be a human being again.

The databurst also contained the early proofs of a paper Dr. Jackson was working on about societal views of Artificial Intelligence, as well as a short video-brief from General O'Neill and a document labeled LtC JOHN SHEPPARD EYES ONLY.

He opened the document, studied it with a faint smile, and transferred it to a tablet to carry down to the labs.

As expected, McKay and Zelenka were alone in the lab, reviewing the Tria Prima documentation. He leaned in the doorway and waited for them to start arguing about something (never a long wait) before he cleared his throat.

"We must revisit the idea of a bell for you," Zelenka said, without looking up. "Go away, McKay is busy, no time for shenanigans."

"Won't take long," John drawled. "Stick around, Radek, this is for both of you."

Then they did look up at him, Rodney leaning against the desk expectantly. John held up the tablet, shook it a little, and then began reading off it.

_"Dear Colonel Sheppard -- "_

"Fan mail," Rodney snorted, turning back to his computer.

_"They said I could write to you once the surgery was over and I was feeling better. I wanted to write to Doctor McKay and Doctor Zelenka too, but yours was the only email address I had. Guess you guys must be posted somewhere pretty dangerous if they've classified your email,"_ he continued, ignoring Rodney's dismissive wave. _"My name's Captain James Thatcher, and they tell me I'm the second man in the world to have a computer for a brain."_

Whatever McKay's hands had been doing, they stilled; Zelenka was listening, head cocked.

_"One of the doctors gave me your book,"_ John continued, " _and I wanted to say thank you. And to Dr. McKay and Dr. Zelenka for inventing all this. I guess you know it's not the easiest thing and I've got a lot to adjust to, but it beats being dead and that's what's important."_

McKay snorted, but it was less derisive now.

_"Hope this letter finds you well. Tell the Doctors thank you from me. I think it's a good thing they did here. Guess my two-year-old probably thinks the same. Sincerely, Captain James Thatcher, USAF, 332d AEW."_

He looked up to find both men at a loss for words, practically an unheard-of event.

"Blatant romanticism," McKay said finally, not quite meeting John's eyes. "My heartstrings remain oddly un-tugged."

"Well, Rodney, that's because you have no soul," John replied, grinning.

"Excuse me," Zelenka said, also not meeting anyone's eyes and sniffling suspiciously. "I think I will go find something to eat in the mess."

John stepped aside to let him out the door, then closed the space between himself and Rodney in a few swift steps.

"Hey, Dr. McKay," he said, and Rodney looked up. "Think you did a good thing? Got your very own tin soldier, clockwork man -- "

"John -- "

"Yeah," he agreed, though he wasn't sure it had been meant that way. "Got me."

There was a sort of peace in kissing Rodney, in letting his thoughts fall away until the only thing left was the single code, the one he'd written himself -- _Protect Listen Love Desire Mine Mine Mine Mine Mine_.


	5. Story Notes

_Those who have crossed  
 ___With direct eyes, to death’s other Kingdom  
 __Remember us—if at all—not as lost  
 _Violent souls, but only  
 _As the hollow men  
\-- TS Eliot, The Hollow Men__

In the words of Matt Albie, _this was not the comedy we intended to do when the week began._

The fic grew out of a discussion of SGA on my livejournal specifically focused on Sheppard, and how most of the time he's a total sociopath (this thread has since been lost in the Great Hack of 08). I hadn't seen more than one or two episodes at that point, and so as I watched I spent a lot of time studying how Sheppard interacted with people to see if I could get a handle on it. I determined that he wasn't a sociopath so much as he was permanently stuck at age seventeen, but he definitely acts like a sociopath (as many teenaged boys do) so that's a whole other story (and it's called **[John](http://khohen1.livejournal.com/648932.html)** , and it's by kHo, and it's fantastic).

The end result was that people said there were a lot of fics out there where Sheppard was either 1. crazypants or 2. an actual robot. Having read a great deal of SGA fanfiction, I know item #2 to be a complete lie. But I was fascinated by the idea of it, so I realised I was going to have to write it myself.

I had intended for it to be a short, primarily creepy, perhaps slightly amusing vignette, or a series of short scenes getting into Sheppard's (tin) head, but the more I thought about how all this would work, the longer and more elaborate the story got. I'm not sure in the end there's any actual point in setting it in the SGA universe as opposed to just rewriting it as fiction, but if I spend one more minute working on it I will _kill myself_ , so there you have it.

The original working title of the fic was simply Robot John (I have a knack for the obvious) and then Tria Prima, but as I hate to use titles that are cleverly incorporated into the text I decided against it. I thought about quoting Eliot but finally settled on The Difference Engine after **[Babbage's creation](http://en.wikipedia.org/wiki/Difference_engine)**.

Isaac Asimov **[really did](http://en.wikipedia.org/wiki/Robotic#Etymology)** invent the term "robotics" (by accident). The Matrix does suck and McKay disdains it rightly.

Because I was writing the story literally along with the episodes as I watched them (not my favourite technique -- it feels a bit jumpy and overly referential to the show) there were a lot of scenes I cut or discarded as inappropriate. I saved some of them, god knows why; normally I don't.

***

_This was supposed to fall just before their return to Earth to close the book on the first Tria Prima trial. I couldn't figure out where the hell to take it, but I like the idea of it._

One of the Anthropologists that came in the last wave to Atlantis had begun a map of the Pegasus Galaxy, carefully locked and on a non-networked computer (John's insistence). Each planet they'd visited was marked in orange, and a spiderweb of blue lines connected each planet to its trading partners. It was an impressive piece of work, whatever Rodney had to say about voodoo-worshippers.

The people of Pegasus were traders and talkers. They wandered, they gossipped; word had long ago spread about the black-clad visitors who traded medicine and goods for food and basic supplies. Never broke agreements, and helpful folk in a pinch; it was rumoured that they lived in the city of the Ancients, and they guarded their gate pretty thoroughly so it might be true.

Ronon, trained in the military, had carefully edited out any references that could identify John, as well as his real name, when he translated _The Modern Prometheus_ into Satedan. He was not so careful about who he shared it with; it was Atlantis all over again, where he gave a copy to one of the few straggling Satedans who had survived, and the Satedans thought it was a decent work of heroic epic about a man with a mechanical brain so they shared freely out of it with their acquaintances. It was translated into Kelari next, and one of the scribes of Kel translated it into a subdialect of Athosian that was the Lingua Franca in a significant portion of the galaxy.

Many of the people in that sector had met the visitors, and it wasn't exactly difficult to pinpoint Rodney McKay as one of the alchemists who had built the clockwork man. His companion, Colonel John Sheppard, was almost equally as recognisable. They treated him with a certain amount of curiousity, those who had only heard the rumours, but he looked and walked and talked like any other man. The peaceful people of the galaxy left him to his own devices, and the ones who were less peaceful had more pressing concerns than whether this man with the gun was a wind-up toy.

Occasionally someone would sidle up to him, after a communal meal or early in the morning, and proffer a tightly-wound scroll or a rough-paper book with a hand-stitched cover. He was never certain what to say to them, but he would nod and sometimes flip through the book, looking down at his own words, second- and third-hand in another language.

Finally it occurred to him what he wanted to ask when they showed him the book; he said, to a young man who couldn't be more than nineteen, "What do you think I am?"

"A warrior-priest," he said blankly, as if it were obvious.

Another time, a middle-aged man from a reasonably technologically-advanced society grinned toothily at him. "A prophet of the future?" he suggested.

And another time, the pair of women looked at each other before answering. "An adventurer!"

McKay happened to be checking his equipment nearby, and he rounded the corner as John asked the question; when the two women were gone, he touched the back of John's neck lightly, affectionately, and didn't have to say anything at all.

***

_This is pure self-gratification._

There was only one doctor Rodney really liked, and John suspected it was because he was the only man who had ever managed to stay engaged in a shouting match with him for longer than three minutes.

SGC carefully did not say that he was the best at what he did, but they did say that nobody practiced rigorous failsafe surgical examination like him. If they were going to do this they were going to do it right and if they were going to do it right then the scruffy, sharp-eyed, overmedicated guy with the cane was the one to call.

He reminded John strongly of Rodney. He would have thought the pair of them would be like oil and water, but Rodney respected brains and spine, and Dr. House had those in spades. House respected pragmatism, skepticism, and the inability to ask stupid questions, which were practically Rodney's keywords.

Once they'd stopped shouting at each other they got down to the really precise fighting, the kind you can do with your voice lowered in the mess. John sat between them at meals and actually learned a thing or two about the subtle art of the witty insult.

And he liked that Dr. House didn't treat him as some kind of half-malformed freak like the others, trying to walk a line between curiousity and tact. He treated John like an experiment, which would have been less reassuring if John hadn't seen ample evidence that House was after the truth and wouldn't let politics or human feelings stand in his way. You knew where you stood with people like Rodney McKay and Gregory House.


End file.
